Table of Contents

Since this entire course is devoted to understanding the workings of the cell, it is almost superfluous to dedicate a chapter to identifying the parts of the cell and their functions. However, because it is easy to get lost in the intricacies of the molecules and chemical reactions within the cell, consider this chapter more of a framework or map for the course, giving context to the minutiae.

Biological membranes are the basis for many important properties of the cell, not the least of which is to physically define the cell boundary, and in eukaryotes, the boundaries of each intracellular organelle. However, they are not completely impermeable boundaries, and through embedded proteins, the membrane serves as the gatekeeper for the passage of specific molecules into (e.g. nutrients) and out of (e.g. waste) the cell.

The major functional components of the cell are mostly polymers - long chains of smaller individual molecular units. Each addition of a small link to the chain costs energy. Heterotrophic organisms such as animals ingest food made up of these large polymers, which, when broken down in the digestive process, release energy for maintaining and building that organism. Such chemical reactions, in which complex molecules are broken down to simpler components, are classified as catabolic reactions.

As pointed out at the beginning of this book, most of the energy for life on this planet originates from the sun. In the last chapter, the discussion was on the breakdown of complex molecules such as sugars and fats that hold great, but difficult to access, potential energy to produce molecules like ATP that can act as more readily accessible sources of cellular energy. This energy is then used to synthesize the more complex biomolecules necessary to build living cells.

DNA: the stuff of life. Well, not really, despite the hype. DNA does contain the instructions to make a lot of the stuff of life (proteins), although again, not all the stuff of life. At least not directly. Deoxyribonucleic acid (and its very close cousin ribonucleic acid, or RNA) is a very long chain polymer. You may recall that a polymer is just a really big molecule made by connecting many small similar molecules together).

Although DNA is an excellent medium for the storage of information, the very characteristic that makes it so stable and inherently self-correcting - being double-stranded - also makes it unwieldy for using that genetic information to make cell components. Since the informational parts of the molecule (the nitrogenous bases) are locked inside the ladder, reading it requires the energetically expensive task of breaking all the hydrogen bonds holding the two strands together.

To define a gene, a stretch of DNA must have a promoter, a start site, and and a stop site. In a prokaryote, these are necessary and often sufficient, but in a eukaryote, they are still necessary, but seldom sufficient. This chapter discusses the other elements, both positive and negative, that are used to regulate the expression (i.e. transcription) of a gene. It is primarily a story of transcription factors and the recognition elements to which they bind.

The RNA polymerase has done its job (or in the case of prokaryotes, may still be in the process of doing its job), so now what happens to the RNA? For RNA that is destined to provide instructions for making a protein, then it needs to be translated, which is a job for ribosomes.

Once a polypeptide has been translated and released from the ribosome, it may be ready for use, but often it must undergo post-translational processing in order to become fully functional. While many of these processes are carried out in both prokaryotes and eukaryotes, the presence of organelles provides the need as well as some of the mechanisms for eukaryote-specific modifications such as glycosylation and targeting.

When a eukaryotic cell is taken out of its physiological context and placed in a plastic or glass Petri dish, it is generally seen to flatten out to some extent. On a precipice, it would behave like a Salvador Dali watch, oozing over the edge. However, the cell actually has an intricate microstructure within it, framed internally by the components of the cytoskeleton.

Interactions between a cell and its environment or with other cells are governed by cell-surface proteins. This chapter examines a subset of those interactions: direct cell contact with either other cells or extracellular matrix (ECM). Extracellular matrix is a general term for the extremely large proteins and polysaccharides that are secreted by some cells in a multicellular organism, and which acts as connective material to hold cells in a defined space.

Metazoan organisms are not just conglomerations of cells that happen to stick together. The cells each have specific functions that must be coordinated with one another in order to assure the survival of the organism and thus the shared survival of the component cells. If coordination is required, then a method of communication between cells is also required.

Cells, whether prokaryotic or eukaryotic, eventually reproduce or die.