What makes a cell?

A cell is the smallest unit of life. Everything living is formed of cells, from single-celled organisms, familiar to us as bacteria, to the most complex of creatures such as ourselves, formed of mind boggling numbers of cells, but trivial in comparison to cell numbers in two hundred tons of blue whale. In its role as the basic building block of life, a cell might be considered a relatively simple collection of components, gently ‘ticking over’ to maintain itself and occasionally dividing to create a new cell. Nothing could be further from the truth. Each and every cell, from the simplest to the most complicated, is a self-contained molecular factory working frantically throughout every minute of its lifespan, whether this is the half hour of unique existence of most bacteria before they divide, or the self maintenance and day-to-day activity of our nerve cells, living for several decades. The analogy of a cell as a factory falls somewhat short because, to match cellular activity, the factory itself and much of its machinery would have to be dismantled and rebuilt on a daily basis, without any slowing of production levels. Both animal and plant cells are around a thousand-fold larger than bacteria with a much more complicated and intricate internal organization.

Just what sort of chemistry can support the extreme levels of synthesis that allow the simpler cells to double themselves in minutes, and more complicated cells within a day? At the fundamental level, life is based on the atoms of only six of the 117 known elements: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulphur. Hydrogen and oxygen, combined as molecules of water, make up 99 out of every 100 molecules in the cell. This might appear to make life a rather dilute affair, but some of this water is tightly bound into the structure of larger molecules, and does not occur as actual liquid. Life at the molecular level is based on a restricted set of small carbon-based molecules common for all cells, which include sugars (providing chemical energy), fatty acids (forming cell membranes), amino acids (the units of all proteins), and nucleotides (the subunits of informational molecules such as RNA and DNA). All proteins are formed from just 20 different amino acids, which are common to every living thing. This ‘alphabet’ of amino acids is combined in a variety of different ways similar to the use of letters to make words, forming a massive ‘vocabulary’ of proteins. Proteins exist in a remarkably diverse variety of forms, providing the structural materials, chemical catalysts, and molecular motors that support and drive the processes of life. The code for each unique protein is stored in another code, this time of four letters, which makes up the genes in our DNA and which is passed from mother cell to daughter cell at each division. Each of the 24,000 or so individual genes in our DNA is specific for a single protein, but our bodies may have many times this number of proteins, produced by modifying the original genetic message. Proteins are combined to form multi-protein complexes, the cogwheels and bearings that drive the motors of production and maintenance within the cell. This level of complexity works perfectly for the simpler cells such as bacteria, but in larger and more complex cells such as our own, specific tasks are undertaken in separate sites in the cell termed organelles, which are separated from other components within the cell by their own membranes. Adding yet a further layer of complexity, our own bodies contain 200 or so different cell types.

This book attempts to provide an introduction to the massive diversity undertaken by cells in order to go about their business, and why any (cellular) shortcoming may result in disease.

Basic cell characteristics Everything that lives on the surface of the planet is cellular in nature. At this point we should exclude viruses, as they are unable to reproduce themselves without hi-jacking the synthetic processes of the cell they infect. Their non-vital nature is emphasized by the capacity to make crystals of purified viruses in solution. The cell is the basic unit of life, and as such must fulfil three requirements: (1) to be a separate entity, requiring a surface membrane; (2) to interact with the surrounding environment to extract energy in some way for maintenance and growth; and (3) to replicate itself. These parameters are the same for all living beings, from the smallest bacterium, to any one of the 200 different cell types that create a human being. Many organisms live as single cells, whereas a human has some 100 trillion cells in all. This number can be compared with the total number of people on Earth today (6–8 billion), or even the total number of people estimated to have ever been on the planet (106 billion). As an aid for the perception of these extremely large numbers, we can perhaps use an analogy based on time. One trillion seconds ago equates to approximately thirty thousand years, a time when the Neanderthals were roaming around Europe.

A cell can function perfectly well as a single entity or, alternatively, one cell may be an indfinitesimally small part of a massive community of cells that work together to make a single being such as ourselves. In multicellular organisms, groups of cells form tissues and tissues come together to form organs. Multicellularity requires cells with a complex internal architecture (as we shall see in Chapter 2), whereas the single-celled existence of a bacterium allows for a relatively simple organization (essentially a membranous bag containing the necessary chemical mix to maintain life). When life began, some four billion years ago, the first cells would have been similar to the bacteria of today. However, simplicity doesn’t necessarily indicate primitive or unsuccessful, as bacteria are the most numerous and widespread of cells, and a branch of the bacterial family called Archaea can flourish in the most extreme environments on the planet, where nothing else can survive. In optimal conditions, some bacteria can reproduce every 20 minutes—a rate that will produce 5 billion bacteria in 11 hours, a number equivalent to the world’s total human population. We ourselves are colonized by bacteria to the point where we house ten times the number of bacterial ‘guests’

(mainly in the gut, and weighing around one kilogram) than the number of actual cells in our own bodies.

Membranes and cell walls

As the basic unit of life, every cell must be a discrete entity and consequently requires its own boundary. This boundary is common to all life forms and consists of a thin membrane built from two layers of fat molecules (lipids) and coated and pierced with proteins that control the molecular traffic between the cell and its surroundings. Animal cells are usually combined to form tissues (for example, our skin), involving large numbers of different cell types. The membranes of these cells are in direct contact, held together at specific attachment sites, with other membrane areas modified to allow communication between adjacent cells. Unicellular organisms such as bacteria usually have an extra ‘cell wall’ outside of the membrane, often incorporating adhesive materials to ‘glue’ them to other cells or to surfaces (such as our teeth). Plant cells have a rigid cell wall woven from long molecules of cellulose. This major difference between plant and animal cell structure is largely the reason why animals move and plants (generally) do not.

Plant cell walls provide a strong mechanical framework as well as protection against pathogens and dehydration. Plant cell walls are attached to each other by a glue made of pectin polysaccharides (the chemical that makes fruit preserves set), and further strengthened by the deposition of long strong molecules of celluloses and lignins that are the basic materials for the timber and paper industries. The rigidity of this type of construction allows massive and persistent growth (e.g. the giant sequoia trees of California) or longevity for thousands of years (e.g. bristlecone pines), but at the same time restricts plants to a rooted existence, although their leaves are well able to alter position to optimize exposure to sunlight.

1. The sizes of atoms to relative simple worms on a log scale. Atoms are measured in ?ngstroms, a ‘dead’ unit that is one tenth of a nanometre, but still in daily use by biophysicists

The interior of the cell

In comparison to bacteria, plant and animal cells are massive, about one thousand times the volume.　Figure 1 shows the scale of cells in the units they are measured in: nanometres (one millionth of a millimetre) cover the molecular sizes of cell components, and whole cells are usually tens of micrometres (one thousandth of a millimetre) in length. Plant and animal cells are also infi nitely more complicated, containing a variety of structural elements built from proteins and several types of internal membrane-bound bodies called organelles ( Figure 2 ). Individual organelles have

2. Diagram of the contents of a cell

Centrosome (CE)—a pair of centrioles which organize microtubules according to the requirements of cell shape, movement, or division.

Cytoplasm (Cy)—all cell contents are suspended in a viscous fluid called cytosol.

Endoplasmic Reticulum (ER)—an extensive network of fiattened membrane sheets. Rough endoplasmic reticulum (RER) has ribosomes for protein synthesis, smooth ER (SER) is involved in lipid metabolism.

Extracellular matrix (ECM)—material deposited outside the cell membrane, either as a thin layer, or larger amounts, such as collagen or bone.

Golgi Apparatus (GA)—a roughly circular stack of membranes which receives freshly synthesized proteins from the ER for modifi cation, packaging, and distribution.

Lysosomes (L)—vacuoles containing lytic enzymes for breakdown of ingested material or cell debris.

Microfilaments and Intermediate filaments (Mf, If)—form the cytoskeleton, in combination with microtubules to bring about shape changes and cell movement.

Microtubules (Mt)—dynamic cytoskeletal components, which are constantly assembled and broken down to provide rigidity within the cytoplasm, and act as ‘rails’ for intracellular transport.

Mitochondria (Mi)—are the sites of energy generation for all cellular activity.Nucleus (Nu)—contains the ‘blueprint’ for all cell activity, stored in code on the DNA, which necessitates constant and intense interaction with the cytoplasm.

Nuclear envelope (NE)—the double membrane separating nucleus and cytoplasm. The outer membrane is continuous with the endoplasmic reticulum.

Nuclear pores (NP)—thousands of channels in the nuclear envelope that control the rapid exchanges between nucleus and cytoplasm.

Nucleolus (No)—site of concentrated RNA and ribosome production.

Plasma membrane (Pm)—a lipid bilayer interspersed with proteins which encloses the cell, with specialized sites for attachment and communication with neighbouring cells.

Ribosomes (R)—numerous (millions per cell) molecular machines that assemble proteins.

Vacuoles and vesicles (V)—a variety of membrane-enclosed compartments, which fulfll specialized functions in particular cells

specific functions. Mitochondria, for example, produce the energy for all of the cell’s activities from the breakdown of food molecules in animal cells. Plant cells uniquely have chloroplasts, which convert sunlight and CO 2 into sugars as an energy feedstock for their mitochondria. Both mitochondria and chloroplasts may themselves have been free-living organisms early in evolution, before becoming permanently incorporated into a larger, complex cell. Every cell has a ‘blueprint’ for its own creation coded by the DNA of its genes. In any particular organism, the DNA information content is the same in every cell type, whether they are brain, gut, or skin cells. Most cells (somatic cells) contain two copies of each DNA molecule (they are said to be diploid), except the germline cells (eggs and sperm) in which DNA exists as a single copy (these germline cells are haploid). When egg and sperm fuse to produce the first cell of the embryo (the zygote), two copies of the DNA are restored. How the DNA content of haploid sperm and egg cells is reduced will be discussed in Chapter 4.

In bacteria the DNA is circular, and lies naked within the cell contents, but in plant and animal cells it is contained within an organelle known as the nucleus (from Latin　nucula , ‘little nut’), where it is folded into chromosomes. Cells with nuclei are termed eukaryotes (a Greek word, meaning ‘true kernel or nut’), whereas prokaryotes (from Greek, ‘before nuts’) such as bacteria have relatively little specialization of their contents into discrete internal organelles.

All cells reproduce themselves by splitting into two. Some bacteria manage to increase their contents rapidly enough to undergo division by a process known as binary fission in as little as 20 minutes. The much larger eukaryote cells may　take the best part of a day to double their size before division. Cells as machines have an unparalleled efficiency of performance and diversity of components. The basic building blocks of cell are protein molecules, and every cell has tens of thousands of different proteins, in millions of copies. Actual numbers of the various molecules in a eukaryotic cell are extremely difficult to quantify, but estimates do exist for bacteria, which have 40% of their volume made up of around one million molecules of soluble proteins. A variety of five million small molecules account for 3%, then DNA 2%. The cell membrane and outer bacterial cell wall make up 20%, and the remainder of the contents are made up of the molecular machinery needed to synthesize proteins, including 2000 ribosomes. These figures can be roughly scaled up 1000-fold for the increase in volume of animal and plant cells, which may contain hundreds of individual organelles such as mitochondria, and around ten million ribosomes. Ribosomes are small molecular machines that provide for the assembly of new protein, a crucial requirement in cell maintenance and the provision of new protein prior to cell division.

It is hard to find man-made machinery that matches the workings of an average cell. Perhaps the biggest supercomputer on Earth would come close, but it would also need the ability to physically reproduce itself with faster and faster processors. While this may sound an extreme statement, it becomes more reasonable when you consider that cells have had around four billion years to get their act together, constantly driven by the unremitting pressures of natural selection. In simple terms, natural selection means that if a cell adapts to its environment, feeds and reproduces, then it survives, but failure means death. This process has produced a self-propagating, self-maintaining and repairing system that functions with a level of efficiency rarely approached by man-made machinery. Much of the entire subject of nanotechnology—the engineering of functional systems at a molecular scale—is aimed at replication of molecular reactions with the efficiency levels found in living cells. As well as their highly efficient metabolism (life-sustaining chemical activity), cells are also capable of producing unmatched structural rigidity, as found in the cells that give wood, palms, and bamboo values of mechanical performance that are exceptional in comparison to man-made equivalents(skyscrapers in the Far East often use local bamboo rather than steel scaffolding).

Tissues and differentiation

The main characteristic of eukaryotic cells is their ability to alter their shape, components, and metabolism to fulfll a particular task—to differentiate—a facility which allows them to come together and form multicellular tissues, to combine those tissues into organs, and then form an entire organism such as a human being. We are formed from around 200 different types of cells which make up the four main tissues: epithelia (surfaces), connective tissue (blood, bone, and cartilage), muscle, and nervous tissue. Cells are produced at widely different rates, from sperm (at a rate of 1000 in the same time as a heartbeat) to a nerve cell that may survive a lifetime. Some of our blood cells survive for only eight hours whereas the red cells circulate for about 120 days.

As an example of differentiation, we can briefly consider those cells that form our barrier to the environment. The cells at the surface of our skin have undergone a major ‘remodelling’ (differentiation) to become corneocytes, which are fiattened polygonal plates made mainly of keratin (the same protein that makes nails, hair, and also feathers in birds). Each corneocyte spends about a day at the surface, before being shed and replaced by the one underneath, so that we present a new layer of skin cells to the world every day of our lives. The shed cells are replaced by division of unmodified cells that differentiate as they pass upwards through the 24 cell layers that make up the overall thickness of human skin. Shedding the top layer of corneocytes efficiently removes accumulated debris, along with the 7.5 million bacteria per square centimetre and the various fungal growths that constantly attempt to colonize our outer surfaces. There are 1000 corneocytes per square millimetre, and our overall skin surface area is just under two square metres, leading to a daily loss (and replacement) of around two thousand million cells each day.

The shed skin cells make up about 60% of household dust, and those we lose in bed provide the daily bread of the million or so dust mites that live in our mattresses. Not all parts of our bodies are replaced at this rate, but the skin, our largest organ, provides a good example of the basic properties of cells—replication, division, differentiation, time spent as a functional part of a tissue, and ultimately death.

Are single-cell organisms simple?

In stark contrast to the single purpose in life that a skin cell aspires to, we should consider what life is like for single-celled eukaryotic organisms. Because they are small, they could be considered ‘simple’ and ‘primitive’. To survive, however, they need to seek out food, manage often hostile environments, reproduce, and avoid being eaten by other organisms. Protozoa are the largest group of singled-celled animals with A moeba perhaps the most familiar. Amoebae have been observed to pursue and catch other protozoa such as P aramecium —perhaps the unicellular equivalent of a lion chasing a zebra. Possibly even craftier still are a group of protozoans called Suctoria. These unicellular organisms such as　Dendrocometes paradoxus do not chase their food but instead attach themselves to various surfaces, extend their tentacles, and wait for some unfortunate protozoan, such as a P aramecium , to swim close by. If the tentacles are touched, the ‘prey’ is instantly paralysed, and the contents of its body are sucked down the tentacle into the body of the suctorian, reducing the prey to a shrivelled husk in a matter of minutes. The exact method for the transfer of prey contents is unknown, but it is driven by the spectacular arrays of cytoplasmic structures called microtubules inside the suctorian tentacles (see　Figure　6c ; microtubules will be described in Chapter 2). Having had a good meal, suctoria may choose to ‘mate’, a process requiring the attachment of modified tentacles to each other through which they exchange nuclei (they have one ‘macronucleus’ and three small ones). If bingeing and sex were not enough, D endrocometes has another surprising facility. Dendrocometes lives attached to the gill plates of　Gammarus , a freshwater shrimp.　Gammarus moults regularly, so that Dendrocometes risks being left behind on an empty shell, losing the constant flow of water over the gill plates and the prey that this brings. However, D endrocometes recognizes the earliest stages of moulting (possibly by responding to moulting hormone), and metamorphoses into a form bearing structures known as cilia which allows it to ‘up sticks’ and find a new set of gill plates (cilia will be described in Chapter 2). Thus, ‘simple’ single-celled organisms can have just as complex a lifestyle as that found in many multicellular organisms.

Although protozoa (and single-celled plants) must interact with their environment to survive, their perception is largely limited to physical and chemical interactions at their membranes, but with some interesting features. In single-celled plants such as the green algae　Chlamydomonas , an ‘eyespot’ is visible within the chloroplast under a light microscope. The eyespot is a complex sandwich of membranes with rows of granules that contain around 200 different proteins, including the same rhodopsins found in the retina of our own eye. Signals from the photoreceptive eyespot cause the flagella (whip-like tails on the surface of the algae) to beat in different ways, so the algae swim towards brighter light, but away from light that is too bright. Whilst the eyespot might be thought of as a rudimentary eye, there is no imaging involved, or required, as the eyespot supplies all the information required for the organism’s needs, helping it to cue day/night (circadian) rhythms, and optimize photosynthetic activity.

Tissue culture

An enormous amount of information about mammalian cells has come from　in vitro studies; cells grown in a glass or plastic flask, maintained in a nutrient broth at 37 degrees in an atmosphere of5% carbon dioxide, replicating the conditions in the body as closely as possible. Plant cells can also be cultured, often with their cell wall stripped off. Growth of cells and tissues outside the body goes back as far as the late 19th century, and the methodology for tissue and cell culture was established by Ross Harrison in Baltimore, USA around 1910. Tissues such as lung from laboratory mice embryos usually grow well as single cells, forming ‘primary cultures’, but they almost always have a limited life span, dying off after 50 or so rounds of cell division. Cells that are isolated from solid tissues require attachment to the surface of the plastic growth vessel to divide and grow, but blood cells, which normally exist in a liquid, do not require attachment, and grow as a ‘suspension’ culture. Cells are usually cultured as a single type, but mixed cell cultures such as those grown from isolated bone marrow will both survive and maintain the cellular interactions that occur in the body. When a small piece of solid tissue is excised and put into culture conditions, the cells that grow the most readily are those that respond to wounding in the living animal. These cells, known as fibroblasts, are the cells that maintain connective tissue that forms the structural framework of the body, such as ligaments and tendons. After injury, fibroblasts pull the edges of wounds together, and secrete the collagen that forms scar tissue. In culture conditions they are long and thin, with a leading edge that fans out at the front of the cell as it moves over the growing surface ( Figure　3c ). Within a few days, continuous rounds of cell division cause the surface of the flask to become increasingly crowded, and when there is no more room for newly divided cells to reattach to the growing surface, division will cease. This is called density-dependent inhibition of growth, and is characteristic of normal cells, but not those cells derived from tumours. At this point the cells are sub-cultured into new flasks at a reduced density. Because primary cultures die off after about 50 divisions, this puts a time limit on any series of experiments, so ‘permanent’ cell lines (usually derived from tumours) which divide indefinitely are often preferred by researchers.

3. Cell types and their shape. (a) Haemopoietic (blood) stem cell (spherical), (b) epithelial (polygonal) cell, (c) fibroblast, (d) adipocyte or fat cell. All these cells have been grown in tissue culture. Although the surface of the fat cell is smooth, the other cells are more typical, with membrane folds, ruffles, and finger-like extensions (microvilli) over their surfaces. The difference in size between the fat cell and a normal cell is shown by the round cell at the bottom left. (e) D endrocometesparadoxus feeding on a P aramecium attached to its tentacles

HeLa cells, the first permanent human cell line

Although permanent cell lines from humans are generally derived from tumours, tumour biopsies are notoriously tricky to establish in culture, with about 1 in 100 attempts successful. The first time that human cells were grown in culture as a permanent cell line was in 1951, by George Gey in Baltimore, USA. These were HeLa cells, so called because of their source—a cervical tumour biopsy from a lady called Henrietta Lacks. Henrietta’s condition was diagnosed in Johns Hopkins, one of the very few hospitals in the USA in 1951 that would treat a member of the black population without health insurance. At the time, although cells from tumour biopsies worldwide were constantly put into culture conditions, none would survive longer than a few days. Henrietta’s cells, however, began to double within days, sadly in line with the extremely aggressive and fast growing tumour spreading throughout her body, which killed her within months. The news of Henrietta’s cells very quickly spread around the world of cell biology. In response to the worldwide demand for the first permanent human cell line, the Tuskegee Institute began mass producing the cells, shipping 20,000 tubes or 6 trillion cells every week. This means that every few months, the same volume of cells that had been enough to form Henrietta herself left the production line. HeLa cells were experimented on in every conceivable way, none of which would have been possible using ‘whole’ humans. They were exposed to every drug that might be toxic to tumours, every type of radiation possible, and a variety of toxins and viruses. For the most part they didn’t react in a significantly different way to different species of mammalian cells, but it was important to show that human tissue culture cells did not behave in any unique ways. As her cells have now been grown worldwide for over half a century, there is probably enough of Henrietta (in the form of single cells) around the world for her to populate her own town. In fact one of her daughters, after seeing the film J urassic Park , was briefly convinced that there were ‘copies’ of her mother in London, where she had read that much research had been carried out on HeLa cells. Henrietta’s children would probably never have known about their mother’s cells except that they were tracked down by Johns Hopkins researchers who wanted to compare the DNA from HeLa cells with its closest human match. This interest alerted them to the multimillion dollar industry that had been spawned by their mother’s tumour, and, not unreasonably, they (and their lawyers) tried to extract some money from the situation. Unfortunately for them, in 1951 no rights to patient samples existed, and the state of California has subsequently ruled that ‘a person’s discarded tissues are not their property and cannot be commercialized’. Even now, Henrietta’s children are still unable to afford health insurance in the USA. Despite 60 years of intensive research, including recent DNA analysis, the actual reasons for the prolific nature of HeLa cell growth are still unknown. HeLa cells could almost be considered the ‘weeds’ of tissue culture, having taken over many other cell lines by accidental cross contamination, a fact that only came to light when cultured cells began to be characterized by their DNA some 20 years ago.

For decades, research performed on cells　in vitro has been questioned as to just how representative it is, because cells grow normally in a three-dimensional environment in a moving organism and are subject to a variety of stresses and factors not experienced by a single layer of cells growing in a plastic dish. Remarkably, in over half a century of concentrated research, cells in culture have produced very little in the way of misleading information, and without this accumulated knowledge it is unlikely that the current potential of stem cells for human therapy would exist at all.