Chapter Four

Cell formed out of molecules

In this chapter we see how the large structures of the cell depend upon the properties of their component molecules. We look at two examples:

1) The fat molecules that form the essential structure of the cell membrane (read first).

The cell membrane surrounds and contains the cell. When you analyse the membrane you discover it is comprised (mainly) of two fluid layers of fat molecules.

How did those molecules come to be like this? How do they give the membrane the properties that it has?

2) The protein molecules that, embedded in that membrane, serve as gates and channels through which other molecules may pass.

Another example of how atoms and molecules determine the large-scale behaviour of cell structures lies in the permeability of cell membranes.

Under the right conditions (sometimes including the presence of an energy supply - ATP) cell membranes will pass ions like sodium and potassium, small molecules such as glucose and large molecules like messenger RNA.

Why should a cell membrane be permeable at all when, after all, it is a double layer of molecules?

On examination, the cell membrane has a number of other molecules embedded in it, mostly proteins.

These proteins act as gates or channels through which molecules can be selectively passed.

For example, the molecule glucose needs, on occasion, to be passed from cell to cell. A protein called a permease (it makes the membrane permeable), embedded in the cell membrane, allows glucose to pass.

In order to inhabit a transmembranous position, proteins must have hydrophobic (water-hating) regions that can embed in the bilayer without upsetting the fat tails and hydrophilic regions that are happy to be exposed to aqueous solutions on one or both sides of the membrane.

How do proteins have water-hating regions in just the right place so that they embed in the membrane? How are these membrane bound proteins shaped exactly so they let only certain molecules pass - not merely according to size but according to kind as well?

Proteins are the most capable molecules in the cell and are capable of precisely defined shapes and properties.

PROTEIN STRUCTURE
Proteins are perfectly formed to perform complex tasks in precise ways. They could be molecules made out of atoms arranged to give a rigid structure with a fixed shape and size. In fact, proteins are long chain-like molecules that must fold into their complicated shapes.

How can proteins be counted upon to fold into EXACTLY the right folded shape. The answer is that parts of the chain attract each other whilst other parts actively repel. A more accurate way of putting this is to say that the protein chain flaps around until it comes to rest in the position of lowest energy. The configuration with lowest energy IS its favourite way of folding.

Here a reasonable analogy is with a soccer ball that is kicked onto hilly ground and rolls until it comes to rest in a valley-bottom. The soccer ball is rolling until it comes to rest in the position of lowest energy.

Why do some parts of the protein chain attract each other and others repel? Proteins are long chains of molecules called amino acids. 20 amino acids occur naturally and each amino acid has its own unique properties, properties which make it attract or repel other amino acids. It is the proportions of the different amino acids that a part of the chain contains that determine how it will behave.

The precision with which the linear sequence of amino acids in a protein chain can control its three dimensional structure and properties enables proteins to perform a huge variety of important roles in the cell.

Proteins are heavily involved:

1) as structural features of the cell.

2) as helpers in the activities inside the cell (enzymes) that are capable of controlling chemical reactions by speeding them up - even in cases where they would not not normally occur at all.

One important role that proteins have in cells is as a building material out of which features can be precisely constructed. The shape of cells, their movement, and the positioning and movement of structures within them - these are all made possible by proteins. For example, there's a complex web of fibres in the cytoplasm, still little understood, called the cytoskeleton.

Certain proteins speed up chemical reactions in the cell that would take place far too slowly, if at all, without them. Proteins can catalyse (speed up) reactions by providing within their folds environments that help molecules to interact with each other. Catalytic proteins are called enzymes and in the following diagram there is an indication of how this might work in the case of a simple reaction in which a molecule is split into two parts.

The other important role that proteins have in cells takes advantage of their ability to form precise three dimensional structures.

For example, the molecule glucose needs, on occasion, to be passed from cell to cell. A protein called a permease (it makes the membrane permeable), embedded in the cell membrane, allows glucose to pass.

How do proteins have water-hating regions in just the right place so that they embed in the membrane? How are these membrane bound proteins shaped exactly so they let only certain molecules pass - not merely according to size but according to kind as well?

Proteins are the most capable molecules in the cell and are capable of precisely defined shapes and properties.