STRUCTURE, FUNCTION AND GROWTH OF PROKARYOTIC AND EUKARYOTIC CELLS

The study of cell structure was revolutionised by the invention of the electron microscope. The best optical (light) microscopes can magnify specimens about 1,500 times under optimal conditions. With the electron microscope, magnifications of 100,000 times or more are possible, which enables detailed examination of sub-cellular

components. This structural information, in conjunction with

biochemical studies, has provided a wealth of information about how cells are constructed and how they function.

1.1 Features and ultrastructure of prokaryotic and eukaryotic cells

The great variety that is found in different types of cell makes it difficult to present the ‘average’ cell – there is no such thing! However, there are things that most cells have in common – the presence of genetic material, a cell membrane (plasma membrane), and some type of fluid- based matrix (the cytosol) that makes up much of the internal volume of the cell. We will consider bacterial, plant and animal cells, and try to illustrate the similarities and differences between them. Major aspects to consider are the arrangement of DNA in cells, whether or not sub- cellular organelles are present, the use of membranes within cells, and the organisation of the cytosol.

The bacterial cell

A generalised diagram of a bacterial cell is shown in Fig. 1.1.1. Bacteria are prokaryotic, and therefore lack a true membrane-bound nucleus.

The DNA is present as a single circular molecule, usually termed the bacterial chromosome, although strictly speaking this term should be reserved for the more complex DNA:protein structures found in eukaryotic cells. The DNA is highly condensed or ‘packaged’ by coiling and folding, and this produces a structure known as the nucleoid. Such packaging is needed because of the length of the DNA molecule – a typical Escherichia coli cell is about 1 µm diameter × 2 µm length, yet it contains about 1,400 µm of DNA. Fitting all this into the cell is only possible because DNA is a very long, thin molecule.

Apart from the nucleoid, there is little internal structure evident in bacterial cell micrographs apart from a large number of ribosomes,

SECTION 1

essential for protein synthesis. The lack of internal structure means that the cytosol is effectively the site of all bacterial cell metabolism. This enables bacteria to adapt very quickly to changing nutritional conditions, but does mean that the regulation of genetic and metabolic activity has to be kept under tight control.

Fig. 1.1.1: Diagram of a typical bacterial cell. Not all of the structures shown may be present in all cells.

Bacteria have cell walls that contain peptidoglycan, which is composed of linked disaccharide and peptide units. A major method of classifying bacteria into two groups is the Gram stain, which stains walls according to how thick the peptidoglycan layer is. Thus we have Gram-positive and Gram-negative bacteria, depending on whether or not the Gram stain is taken up by the cell wall. Lying outside the cell wall there may be a mucilaginous capsule, and there may also be projections from the cell surface known as pili or fimbriae. Longer flagella may also be present.

Bacterial cells are often considered to be ‘simple’ cells. Whilst this may be true in terms of the relatively few structural features that are present within the cell, it is certainly not true when you consider the complex chemical activity of the cell, all of which has to happen inside the ‘bag’ of membrane-enclosed cytosol. Most bacterial cells exist as individual

organisms, and need to be metabolically self-contained if they are to survive.

Cells with a true nucleus and other membrane-bound organelles are

known as eukaryotic cells, and are more complex than bacteria in terms

of structure. Many eukaryotic cells are components of multicellular

organisms, and therefore the requirements of the cell are somewhat

different from those in bacteria.

Plant cells

A diagram of a typical plant cell is shown in Fig. 1.1.2. Plant cells show less diversity of form and function than animal cells, and have relatively rigid cell walls with cellulose as a major component. Thus connections are required if cell–cell contact is to be achieved. These connecting structures are the plasmodesmata, which enable a continuous cytoplasmic link to be formed between cells. The region linking two adjacent cell walls is known as the middle lamella.

Fig. 1.1.2: Diagram of a cell from a higher plant. Cell sizes vary considerably in plants, but this would be around 30 × 20 µm.

Distinguishing features of such cells are the cellulose cell wall and the presence of a central vacuole and chloroplasts. (Copyright Philip Harris Education. Reproduced with permission.)

Within most plant cells a central vacuole, which looks essentially empty,

occupies a large proportion of the cell volume (up to 90% in some

cases). The vacuole has a much more important role in the life of the

plant cell than its apparent structural simplicity would suggest. The

membrane surrounding the vacuole has an important function in

controlling the movement of substances into and out of the vacuole,

which can act as a storage reservoir for nutrients, waste products,

enzymes and other metabolites. The vacuole is also important in

maintaining cell water relations and thus cell turgor.

The cytosol of plant cells contains numerous membrane-bound organelles and other structures that are not present in bacterial cells.

The nucleus is of course the most notable, as this characterises the cell as being eukaryotic. The nuclear membrane (or nuclear envelope) is a double membrane structure, with nuclear pores and connections to a network of membrane-bound channels known as the endoplasmic reticulum (ER). This may be either Rough ER (ribosomes associated with the ER membranes) or Smooth ER, which has no ribosomes. The ribosomes function in the synthesis of proteins that are then

transported via the ER channels to different parts of the cell.

A derivative of the ER system is the Golgi apparatus (sometimes called the dictyosome in plants). This is named after Camillo Golgi, who first described it. The function of the Golgi apparatus is to modify and package materials such as proteins and polysaccharides.

All cells carry out various functions that require energy. Energy conversion in eukaryotic cells involves two specialist organelles – chloroplasts and mitochondria. Plants (both algae and higher plants) are the major primary producers in ecosystems, and have chloroplasts that localise the reactions of photosynthesis. The chloroplast has a complex arrangement of membranes arranged in stacks called grana.

These increase the surface area inside the chloroplast and also provide the membranes on which electron transport proteins are localised.

Chloroplast structure can be seen in Fig. 1.1.3, which shows an electron

micrograph of part of a plant cell.

Fig. 1.1.3: Electron micrograph of part of a plant cell, showing the chloroplast. Features labelled are as follows: A – cell wall, B – cell (plasma) membrane, C – starch grain, D – chloroplast stroma with ribosomes, E – a granum (stack of thylakoid sacs), F – DNA strands, G – tonoplast or vacuolar membrane, H – vacuole, I – rough

endoplasmic reticulum, J – cytoplasmic ribosomes, K – chloroplast envelope, L – intercellular space.

Photographed at 50,000 × magnification. (Copyright A.W. Robards/

Philip Harris Education. Reproduced with permission.) The light reactions of photosynthesis provide energy by the

photochemical splitting of water, which is used to drive the synthesis of ATP and NADPH

. These compounds are then available for the dark (light-independent) reactions, in which carbon dioxide is reduced to carbohydrate.

Energy capture in photosynthesis, and the consequent fixing of carbon dioxide into sugar, is the single most important set of reactions in biological systems. Without photosynthesis, there would be no

carbohydrate available to be metabolised in respiration, and thus cells could not survive. In aerobic organisms glucose can be completely oxidised to carbon dioxide and water by the processes of glycolysis and the tricarboxylic acid (Krebs) cycle. The major energy yield in this process occurs during the re-oxidation of NADH

in mitochondria.

These are in some ways similar to chloroplasts in that they have a folded

membrane arrangement on which the electron transport proteins are

arranged to enable ATP synthesis to be driven by proton pumping

mechanisms.

Chloroplasts and mitochondria are essential parts of the biological energy chain, and both illustrate how membranes can be used within cell organelles to increase the area available for the localisation of

biochemical reactions. A comparison of the structure of chloroplasts and mitochondria is shown in Fig. 1.1.4.

Fig. 1.1.4: Comparison of the internal structure of mitochondria and chloroplasts. The use of membranes to increase the surface area/volume ratio, and the presence of DNA, are common features of these two

organelles.

Animal cells

We have already met most of the components of animal cells, as they are similar to those found in plant cells. There are two notable exceptions – animal cells do not have chloroplasts or cell walls. In addition, any vacuoles present are usually very small (and transient) when compared to the plant cell vacuole. Animal cells show a much greater variation in structure and function than plant cells. This variation is however achieved by using the ‘standard’ set of cell components in different ways, depending on the type of cell.

A diagram of an animal cell is shown in Fig. 1.1.5. In addition to the

main components such as the nucleus, Golgi apparatus, endoplasmic

reticulum and mitochondria, animal cells may have microvilli on the

cell surface. They also have centrioles, which assist in the organisation

of spindle fibres during cell division. Some components of animal cells

as revealed by electron microscopy are shown in Fig. 1.1.6.

Fig. 1.1.5: Diagram of an animal cell. This cell would be approximately 20 µm in diameter. Note the lack of a cell wall, vacuole and

chloroplasts. (Copyright Philip Harris Education. Reproduced with permission.)

Fig. 1.1.6: Electron micrograph of cells in rat liver. Features labelled are as follows: A – rough endoplasmic reticulum, B – mitochondria,

C – mitochondrial envelope (highlighted for clarity), D – nuclear envelope, E – nucleus (nucleoplasm), F – part of the Golgi apparatus, G – cell membrane separating two adjacent cells, H –

glycogen granules.

Photographed at 25,000 × magnification. (Copyright A.W.

Robards/Philip Harris

Education. Reproduced with

permission.)

In looking at plant and animal cells, we have seen that the use of membranes to provide internal structure is a central theme. The intracellular arrangement of membranes is often called the

endomembrane system, and can be considered as a way of organising the cytosol so that the complex metabolism required for eukaryotic cell function can be controlled and regulated.

In addition to the main subcellular structures already described for plant and animal cells, there are other organelles and structures found in eukaryotic cells. These include a variety of membrane-bound vesicles such as microbodies (also called peroxisomes) and lysosomes. The function of these vesicles is often to isolate specific reactions which might otherwise be harmful to the cell if they were not kept separate from the rest of the cytosol. Other structures of importance are the elements of the cytoskeleton, namely microtubules, intermediate filaments and microfilaments. We will consider the cytoskeleton in more detail elsewhere in this book.

The organisation of DNA within the nucleus of a eukaryotic cell is more complex than the ‘naked’ DNA found in prokaryotes. Eukaryotes have multiple chromosomes, and the packaging problem that is evident even in bacteria is more pronounced. In human cells, some 2m of DNA must be packed into a nucleus that is about 5 µm in diameter. This is achieved by coiling the DNA around nucleosomes, which are made up of histone proteins. More extensive coiling of the nucleosome chain is required, particularly during cell division, and this produces the tightly packed structures that we recognise as eukaryotic chromosomes.

1.2 Cell growth and the cell cycle

The cell theory states that cells can only arise by the division of existing cells. Cell growth and division is therefore a critical process in the life of cells and organisms. The reproduction of cells, from when the cell is produced by division of the mother cell until the new cell itself divides, is known as the cell cycle. The length of this cycle varies depending on the cell type. Bacterial cells can divide every 20 minutes when growth conditions are favourable, whereas human liver cells only divide about once a year. Mammalian cells in tissue culture have a cell cycle time of about 20 hours; frog embryo cells divide much more frequently with a cycle time of around 30 minutes.

Despite the variation in the duration of the cell cycle, there are certain

basic requirements for cell division. If two new cells are to be produced,

clearly the amount of cell material must double if the daughter cells are to remain the same size as the parent. This is particularly critical for the DNA of the cell, which must be copied exactly if the genetic integrity of the cell is to be maintained. This is achieved by the process of DNA replication, which is an important marker during the cell cycle.

How has the cell cycle been studied? If you were to look at a mammalian cell under the microscope for a complete cell cycle, you would see very little evidence of cytological changes until the last hour of the process, when suddenly there is a flurry of activity as the chromosomes move apart and two new cells are formed. Thus early descriptions of the cycle separated the process into two parts, called interphase and division.

The division process itself is more accurately called mitosis or the M phase of the cycle. Mitosis refers to the separation of the chromosomes, and this is followed by division of the cell during cytokinesis (CK).

Interphase is sometimes called the resting phase, but in biochemical terms this is in fact a very active period of growth. A more accurate description of the cell cycle splits interphase into three parts. The period of DNA replication is known as the synthesis or S phase, and there are ‘gaps’ known as G

and G

. As our knowledge has increased, it has become clear that ‘gap’ is perhaps not the best way to describe these two periods, as this suggests little activity, as does the term interphase. A diagram of the cell cycle is shown in Fig. 1.2.1.

Fig. 1.2.1: The cell cycle.

Interphase is made up of phases

G

, S and G

. During S phase

the DNA is replicated, although

no cytological changes are

distinguished in the light

microscope. The cell grows

during interphase and enters

the M phase (mitosis). The four

sub-stages of M phase are

prophase (P), metaphase (M),

anaphase (A) and telophase

(T). This is followed by

cytokinesis (CK) which

generates two new daughter

cells, each of which enters G

to

begin the cycle again. For

animal cells in tissue culture,

cycle duration is around 20

hours.

Mitosis

The actual division of the cell requires a series of co-ordinated events that separate the replicated chromosomes and then split the cell into two, each half having received a complete set of chromosomes. After DNA replication the chromosomes are composed of two chromatids, held together at the centromere. Following separation during mitosis, the newly separated sister chromatids are known as daughter

chromosomes.

Although mitosis is a dynamic process, there are four stages that can be recognised easily in the light microscope. These are prophase,

metaphase, anaphase and telophase. Movement of chromosomes is achieved by spindle fibres, which are microtubules. These are composed of alternating dimers of α and β tubulin (a protein). The spindle begins to form at prophase, and is organised by spindle poles or centrosomes at the two poles of the cell. During mitosis the spindle serves to guide the daughter chromosomes and pull them apart to opposite ends of the cell. Fig. 1.2.2 shows the events of mitosis in onion cells.

Fig. 1.2.2: Mitosis in onion cells (Allium sp.). Photographs represent cells seen under the light microscope at 100 × magnification. The diagram and explanation describe the events in each stage.

Due to the structural differences between plant and animal cells,

cytokinesis is achieved by different mechanisms in these two cell types.

In animal cells, constriction of the cytoplasm by a contractile ring of actin and myosin produces a cleavage furrow, which essentially pinches the cell into two pieces. In plants the cell wall makes this impossible, and cytokinesis is achieved by the formation of a new cell wall to separate the daughter cells.

Control of the cell cycle

What controls cell division? This is a question that has occupied

biologists for many years, and a wide variety of different organisms and cell types has been used to try to answer some of the main questions.

Obviously it is important that DNA replication is complete before mitosis, and that the cell mass has increased sufficiently to enable two daughter cells to be formed. Also, the division processes of mitosis and cytokinesis have to be controlled in both temporal and spatial terms if success is to be achieved. In multicellular eukaryotes, additional constraints on cell division are required if cell numbers are to be controlled. To divide, these cells require specific growth factors, of which over 50 types have been isolated. In the absence of enough growth factor, cells stop at the G

checkpoint and enter a non-growing phase called G

.

Our current understanding of cell cycle control is that there is a central mechanism that is used to assess the status of the cell as it progresses through the cycle. This mechanism works through a series of three main checkpoints:

• G

checkpoint – towards the end of G

phase, cell size is assessed. If sufficiently large to allow division, the cell enters S phase and DNA replication begins.

• G

checkpoint – the success of DNA replication is monitored, and if all is well entry into mitosis is triggered.

• M checkpoint – this occurs during metaphase and triggers the exit from mitosis and cytokinesis, and entry into the next G

phase in the daughter cells.

The molecular mechanisms that control the cell cycle involve the

interactions of many different genes and proteins to ‘trigger’ the events

of the cell cycle in their proper sequence. For example, a critical part of

cell division is the entry into mitosis. This is triggered by a complex

called mitosis promoting factor (MPF), which in turn is controlled by

other intracellular cell cycle signals.

Abnormal cell division: cancer cells

Cancer cells are those in which the normal control of cell proliferation has been lost, enabling these cells to form tumours. Although often not the only defective function, this loss of cell cycle control is a major feature of cancer cells. There are two main classes of genes that can generate abnormal cell division. Proliferation genes encode proteins that promote cell division, and any over-expression of these genes could result in excessive cell division. Genes in this category are called

oncogenes when mutated (proto-oncogenes when normal). The second class of cancer-causing genes are known as antiproliferation genes, which normally help to restrict cell division by acting at cell cycle checkpoints. These genes are sometimes called tumour-suppressor genes. In diploid cells, only one copy of a proto-oncogene has to mutate into an oncogene to cause a problem, whereas both copies of a tumour-suppressor gene would have to become abnormal. Thus

mutations in proto-oncogenes are dominant, those in tumour-

suppressor genes are recessive. Our knowledge of how cancer cells arise has developed greatly over the past few years, and many types of proto- oncogene and tumour-suppressor gene have been identified.

1.3 Differentiation of cells into tissues and organs

Although the cell is essentially a complete living system in its own right, in multicellular organisms cells are organised into tissues and systems for specific functions such as support, movement, nutrition, co- ordination and control. Much useful information about tissues and systems has been obtained by studying the final product – liver, kidney, nerves, glands and so on – but the key question is concerned with how these tissues and systems arise in the developing embryo. This is the area of developmental biology. When scientists began to isolate and study genes, a logical step was to try to understand how genes function in the control of developmental processes. Thus the field of

developmental genetics has emerged as one of the central areas of modern biology. Despite great advances in our knowledge,

development remains one of the most complex and astonishing branches of science.

One way of looking at complex processes is to study simple organisms, to see if any functions correlate with those in higher organisms.

Although there are not many developmental processes evident in

bacteria, some aspects of how genes are expressed have become clearer

by looking at adaptive responses such as expression of the lac operon.

Multicellular plants provide relatively well-ordered systems, with much simpler developmental patterns than animals, yet development in plants is not as well understood as in animals.

Development in animals begins with a single fertilised egg undergoing successive divisions. Cell proliferation is of course needed to make up the cell number required as the embryo develops – an adult human has more than 1,000,000,000,000 cells! However, all these cells divide mitotically, and so have identical genomes. So how do different cells arise? And how do they end up in the correct place as the embryo grows?

Differential gene expression in development

To generate different cells from the same genetic information, there must be some sort of control over gene expression. This control can be both temporal (different genes expressed at certain specific times in development) and spatial (cells in different places in the embryo

expressing different genes). Development is not a fixed series of genetic events, but rather a ‘conversation’ between cells as the embryo

develops. This ‘conversation’ involves gene products, which influence cellular events, which in turn create patterns due to cell movement and differentiation. Unravelling all this complexity is an immense task, but it is becoming clear that similar processes operate in all animals. Studies on the fruit fly Drosophila melanogaster have enabled researchers to gain an almost complete understanding of how genes influence development in this organism. We will look at some examples to illustrate.

Segmentation in Drosophila

The body of a mature Drosophila has 17 segments. These are established early in development by the action of several genes in a hierarchical sequence where the action or effect of one set of genes depends on the effects of genes earlier in the developmental sequence. In Drosophila, the first set of genes produce gradients of concentration of gene

product which determine the anterior/posterior and dorsal/ventral axes.

The next set of genes respond to these gradients to divide the embryo into four main segments. The action of yet other genes further sub- divides the embryo, and then sets up the final segmentation pattern. At this time regulatory (homeotic) genes control structural genes to

determine the final fate of each of the segments by specifying the type of appendages and other structures that are specific for each segment.

Gene action in Drosophila pattern formation is summarised in Fig. 1.3.1.

Fig. 1.3.1: Differential gene expression during pattern formation in Drosophila. The developing embryo is divided into smaller and smaller segments by the sequential action of different sets of genes.

Embryological development in vertebrates

In addition to differential gene expression, other factors are important in development of the animal embryo. In vertebrates, the fertilised egg divides to produce a ball of cells called the blastula, which then folds in on itself during the process of gastrulation. This sets up the major body plan of the embryo, and by a ‘conversation’ process similar to the

Drosophila example, cells interact with each other, move and differentiate to give progressively higher degrees of order in the

embryo. A schematic representation of this series of events in the mouse

is shown in Fig. 1.3.2.

Fig. 1.3.2: From egg to organism – the sequence of events in the development of the mouse embryo. Vertebrate development involves a series of complex interactions involving differential gene expression, cell signalling, and cell movement.

Developmental biology is a complex and exciting area of biology, that constantly provides new insights into how genes function to provide form and structure in the developing organism. It is clear that

development involves molecular ‘conversations’ between cells, and that it is therefore a dynamic and interactive process rather than a simple reading of the genetic instructions.

1.4 Cell and tissue culture

The ability to grow cells in culture is essential for both pure and applied aspects of biology. The applications of cell culture are many and varied – perhaps growing bacterial cells for a basic gene manipulation procedure, culturing mammalian cells for cancer studies, or producing new plants by using tissue culture techniques. Although there are marked

differences in the techniques and growth media used with different cell

types, there are certain things that are required for all cell culture procedures:

• a source of the cell material – either freshly prepared, or from a stock of the cell line or bacterial culture.

• a suitable container for cell growth – a simple flask may be sufficient, or a sophisticated fermenter with computer-controlled monitoring of culture conditions might be needed.

• a growth medium that provides all the required nutrients.

• opportunity for gas exchange (chiefly oxygen and carbon dioxide).

• control of factors such as temperature and pH.

• a method for measuring cell growth – this might involve counting cell numbers in the culture, or measuring the optical density in a

spectrophotometer.

• avoidance of contamination of the culture with unwanted micro- organisms.

Let’s look at some aspects of cell and tissue culture using micro- organisms and mammalian cell lines as examples.

Micro-organisms

Microbes inhabit many diverse ecological niches, and we might therefore expect that they should be adaptable and relatively easy to culture in the laboratory on a small scale (up to a few litres of culture). In addition, many types of microbe are used in the biotechnology industry in processes for the production of useful compounds. Industrial scale operations can involve culture volumes of up to tens or even hundreds of thousands of litres. The term fermentation is often used to describe any micro-organism growth procedure, although technically the term refers to anaerobic growth only.

Unicellular algae have few requirements, and can be grown in simple mineral salts media. Bubbling with air (often enriched with carbon dioxide) increases the growth rate and yield of these photoautotrophs.

Bacteria and yeasts need more complex media, as they are

heterotrophic and therefore need an organic carbon source and other compounds such as amino acids.

Micro-organisms can be grown in batch culture, where a culture is grown without dilution until maximum attainable density is reached.

Batch cultures under appropriate conditions show a period of

exponential growth, but this becomes limited by nutrient availability or cell density effects. Cultures then enter a stationary phase and

eventually die if not sub-cultured.

Exponential growth can be maintained in continuous culture if conditions are altered as growth continues. This can be achieved by continual addition of fresh medium and removal of an equal volume of the culture.

Mammalian cell culture

Animal cells are fragile and require more carefully controlled conditions than microbial cells if growth is to be maintained. Growth media are more complex, although the basic requirements are similar to those for bacterial cells. The minimum growth medium recipe consists of a

balanced salt solution with amino acids, vitamins and glucose. Useful additions are a pH indicator and antibiotics to prevent bacterial growth, but the main additional requirement is for animal serum such as foetal bovine serum (FBS). This is difficult to define chemically, but many of the components appear to be essential for animal cell proliferation.

Animal cell technologists have been trying to establish defined media for cell culture, but to date only a few cell types are supported by serum- free media. Growth media containing 5–10% FBS are often used for cell culture.

Cells can be obtained by treating tissue samples with a proteolytic enzyme (such as trypsin) to separate cells from each other. This gives a primary cell culture, from which secondary cultures can be derived.

However, one drawback is that normal cells only divide a finite number

of times before they die, and thus long-term culturing of primary cell

cultures is difficult. The most common cell lines used today have either

been derived from tumours or have been transformed to produce

immortalised cell lines. These cell lines are neoplastic, that is they

produce cancers if transplanted into animals. Some common animal cell

lines are shown in Table 1.4.1.

Table 1.4.1: The origin and properties of some commonly used animal cell lines. Cells generally grow as monolayers in tissue culture flasks.

Those that are able to grow in suspension culture conditions are indicated.

Cell line Species of Tissue of Cell Growth in

origin origin morphology suspension?

3T3 Mouse Connective Fibroblast No

CHO Chinese hamster Ovary Epithelial Yes

BHK21 Syrian hamster Kidney Fibroblast Yes

HeLa Human Cervical Epithelial Yes

carcinoma

Cells in tissue culture generally grow as a monolayer adhering to the bottom of the plastic flask used as the culture vessel. Animal cells growing in culture are shown in Fig. 1.4.2. When the cells cover the available surface, they are said to be confluent, and proliferation stops until cells are sub-cultured into fresh medium.

Fig. 1.4.2: Animal cells growing in tissue culture. The cells form a flat sheet or monolayer on the bottom of the culture flask. One cell is outlined with a white border, showing the boundary of the cell (formed by the cell membrane) and the nucleus.

(Courtesy of Dr Dajiang Li.)

One of the main advantages of growing cells in culture is that they can

be selected and cloned – that is, a culture of identical cells can be

derived from one isolated cell. This has been useful for the isolation of

mutant cell lines, which can be used to understand normal cell growth

processes and may also be useful in biotechnological applications. In addition, cell lines can be fused to produce new hybrid cells which often have useful characteristics.

1.5 Plant tissue culture

Plant cells can be grown in culture in a similar way to animal cells,

although the growth requirements are simpler and defined media can be prepared more easily. One particularly useful trait of plant cells is their ability to regenerate complete plants under appropriate conditions. In theory, all somatic cells from multicellular organisms have this potential, as they have the same genome – this is called nuclear totipotency.

However, animals are much too complex to regenerate directly from somatic cells, and thus the applications of regeneration have been restricted to plants. Many commercially important ornamental plants are propagated in this way. Tissue culture is also important in the

production of pathogen-free plants.

Small pieces of plant tissue (explants) can be taken and grown on a medium containing plant growth regulators (plant hormones) such as auxin and cytokinin. Cell proliferation produces an undifferentiated mass of cells known as a callus. By sub-culturing and changing the balance of growth regulators, the callus tissue can be coaxed into differentiating into shoots and roots, and can be planted out to

regenerate complete plants. Callus tissue with developing shoots can be seen in Fig. 1.5.1.

Fig. 1.5.1: Plant cell culture. This shows cells of potato growing on a

petri dish in callus form. The cultures were derived from protoplasts of

the potato cells. The formation of shoot tissue from some of the calli can

be seen. (Courtesy of Dr Y Hamidoghli)

Hybrid plant cells can be generated using a technique known as

protoplast fusion. A protoplast is a plant cell with the cell wall removed enzymatically. This enables cells to fuse together if conditions are

favourable, and thus new combinations of cells can be produced.

Protoplasts are also useful for gene manipulation procedures in plants, as the lack of a cell wall means that recombinant DNA can be readily taken up by the cell. Protoplast fusion is shown in Fig. 1.5.2.

Fig. 1.5.2: Fusion of protoplasts from two different species of potato.

One unfused protoplast (U) is shown, lying on top of another. Compare this with the two heterokaryons shown (H). These are produced when two protoplasts join together during fusion. (Courtesy of Dr Y

Hamidoghli)

SECTION 2

Information about the ultrastructure of cell components, obtained by using the electron microscope, has provided much useful detail about how cells are organised. However, to get a full picture of how cells work, it is necessary to examine the biochemistry of the various molecules and structures found inside cells. The development of biochemical and molecular analysis has followed a similar path to that for microscopy, with more detailed information becoming available as more sophisticated techniques were developed.

Much of the structural information about biological molecules has come from an understanding of their fundamental chemistry. This approach has been extended by studying how these molecules function in their biological roles, which has enabled the elucidation of the many

metabolic pathways that are required for cells to function. Modern developments in molecular genetics can now provide information about how genes work at the molecular level, and thus in many cases the complete picture of how a particular molecular system functions at the cellular level is becoming clear. Many of the important discoveries of recent years in areas such as developmental biology and cancer have come from this approach, which is sometimes called molecular cell biology.

In this section we consider the main groups of molecules that are found in cells – carbohydrates, lipids, proteins and nucleic acids. We then consider two important cellular systems; cell membranes, and the cytoskeleton.

Making and breaking – the molecular architecture of cells

One central theme runs throughout biochemistry – the making and

breaking of chemical bonds. Living systems are composed of a limited

number of elements, with carbon, hydrogen, nitrogen, oxygen,

phosphorus and sulphur (CHNOPS) making up around 99% of their

mass. The carbon atom is of central importance, as it can form four

covalent bonds with other atoms. This enables a variety of complex

molecules to be constructed. In addition to the chemistry of carbon

itself, there are many important functional groups associated with

biological molecules. Some of these are shown in Fig. 2.1.

Fig. 2.1: Some functional chemical groups that are important in biological systems. Groups such as the carboxyl, amino and phosphate groups can be ionised, and thus carry a charge at neutral pH. The ionised forms of these groups are shown alongside the non- ionised version.

Many biologically important molecules are polymers, composed of smaller units called monomers linked together. Two monomers are joined by removing the elements of water. This reaction is a

dehydration synthesis (a specific type of condensation reaction) and can be reversed by adding back the elements of water by hydrolysis.

This feature of being able to construct and de-construct large molecules or macromolecules is one of the most important aspects of cell

metabolism (see Fig. 2.2).

Fig. 2.2: The monomer/polymer cycle. Monomeric units can be joined

together by dehydration to give polymers. Hydrolysis reverses this and

regenerates the monomers. Cyclical polymerisation/depolymerisation

like this is important in many cellular processes.

Making and breaking chemical bonds involves energy. A broad generalisation is that making more complex structures from simpler precursors requires energy (anabolic or biosynthetic reactions) whereas breaking bonds releases energy (catabolic reactions). Where there is little overall energy change, reactions are said to be reversible.

The metabolism of a cell involves a complex mixture of these three types of reaction, all interacting with and responding to different

concentrations of reactants and products, and the whole lot having to be very tightly controlled if energy chaos is to be avoided. The wonder of metabolism is that it works at all!

In considering the structure of biological molecules, it is important to remember that these are three-dimensional arrangements of atoms. In fact, all the reactions in cells depend on the shapes of molecules, so this is a critical point. Whilst it is often difficult to represent 3-D structures in 2-D form (i.e. diagrams), there are a number of conventions that can be used. We will come across some of these as we look at the molecules and macromolecules of the cell.

2.1 Carbohydrates

The carbohydrates are composed of carbon, hydrogen and oxygen in the ratio 1:2:1, giving a molecular formula of (CH

O)

for most simple carbohydrates. These are the monosaccharides or ‘single sugars’. There is considerable variation in monosaccharide structure, based on the number of carbon atoms and the arrangement of the hydrogen and oxygen atoms attached to them. We will examine the most common monosaccharide that is of central importance in biological systems – glucose.

Glucose (C

H

O

) can be defined by its six carbons (making it a hexose sugar) and by the arrangement of the carbonyl (C=O) group at the terminus of the molecule. A different arrangement of the carbonyl group gives a different spatial arrangement of the atoms of a hexose sugar. All these variations of the same C

H

O

formula, known as isomers, make carbohydrate structure a complex topic.

The simplest representation of glucose is the straight-chain form, shown

in Fig. 2.1.1. By convention, if the OH group on carbon 5 (C5) projects

to the right, the form is the

-form; if to the left, the

-form. Most sugars

used in biological systems are the

-forms. Thus the representation in

Fig. 2.1.1 is designated

-glucose. However, in solution glucose adopts a

predominantly cyclical form, where C1 and C5 are linked through the

oxygen atom to give a ring structure. Depending on the arrangement of the hydroxyl group on C1, this generates two further variations known as the alpha and beta structures. In α-

-glucose the hydroxyl group attached to C1 is below the plane of the ring, in β-

-glucose the hydroxyl group is above the plane of the ring. In solution the equilibrium

proportions of the three forms are approximately 38%

α-

-glucose and 62% β-

-glucose, with at any given time only about 0.02% straight-chain form, with some other minor derivatives possible.

Fig. 2.1.1: The straight-chain form of glucose. The carbon atoms are numbered 1–6, with the carbonyl group at C1.

As if trying to make sense of carbohydrate structure wasn’t difficult enough, 3-dimensional representations give a better idea of what the molecule actually looks like. Fig. 2.1.2(a) shows a full representation of the structure of α-

-glucose, with Fig. 2.1.2(b) showing β-

-glucose in the standard shorthand version that is commonly used when drawing

carbohydrate structures.

Fig. 2.1.2: Haworth projections of the glucose molecule. (a) shows α-

-glucose with the carbons and hydrogens shown. The thicker lines show the 3-D effect. (b) shows β-

-glucose in the simplified form. Here, the carbons and hydrogens are not shown (unmarked corners represent carbon, unmarked line ends hydrogen). In addition, the 3-D line

thickenings are not shown. It is assumed that the ring projects with the bottom edge towards the viewer. The OH groups that define the α and β forms are shaded.

The glycosidic bond

Two monosaccharides can be linked by a dehydration synthesis to give a disaccharide. These are defined by the component momomers and by the way in which the bond is arranged. If we consider two glucose monomers, the bond will be between the C1 of one molecule and the C4 of the other, giving either an α(1,4) linkage (maltose) or a β(1,4) linkage (cellobiose). These disaccharides are shown in Fig. 2.1.3. Other disaccharides include common table sugar sucrose (glucose and

fructose), and the milk sugar lactose (glucose and galactose).

Fig. 2.1.3: Disaccharide structure. Two glucose monomers can be joined by an α(1,4) linkage to give maltose. If the linkage is a β(1,4)

arrangement, this give cellobiose The H/OH configuration on the C1 on the right hand side of the diagrams is not specified, as this can exist in either the α or β arrangement.

Polysaccharides

Joining more monomeric units together produces larger polymers. If the repeating units are the same, we have a homopolymer, whereas different subunits give a heteropolymer. Long chains of simple sugars give the polysaccharides. There are many types of polysaccharide, including starch, glycogen and cellulose. These are all homopolymers made from glucose monomers linked together, but have markedly different properties and functions. This again illustrates how diversity of form and function can be generated by relatively simple variations in the chemistry of the molecules. The structure of these three examples is shown in Fig. 2.1.4.

Fig. 2.1.4: Polysaccharide structures

found in starch (amylose, helical

arrangement), glycogen (branched)

and cellulose (parallel chain

arrangement). Each of these is

composed of a chain (or chains) of

glucose monomers.

Glycogen (animals) and starch (plants) are storage polysaccharides, readily hydrolysed to release the monomers for catabolic breakdown to provide energy. Cellulose is a much tougher arrangement of fibres that is ideally suited to its structural role in plants. It is the most abundant organic material on earth, yet most animals lack the enzyme cellulase that is needed to break it down into its component monomers. Other polysaccharides include chitin, a homopolysaccharide found in fungal cell walls and insect exoskeletons, and the glycosaminoglycans, which are heteropolysaccharides found in skin and connective tissues in vertebrates.

2.2 Lipids

Lipids are important in cell membrane structure, and also as hormones and energy storage molecules. The common defining feature of lipids is that they are insoluble in water. Fats and oils are familiar lipids that we use every day, the distinction being a rather arbitrary one of the physical state of the molecule at room temperature.

Although lipids are certainly smaller molecules than the large

polysaccharides, proteins and nucleic acids, they are generally classed as one of the four groups of macromolecules. Three types of lipid are of particular importance in cells: triacylglycerols (or triglycerides), phospholipids and steroids.

Triacylglycerols

The constituents of triacylglycerols are a glycerol ‘backbone’ and fatty acids. Glycerol is a 3-carbon alcohol; fatty acids are hydrocarbon chains ending with a carboxyl group. If all the available bonds are occupied by hydrogens, the fatty acid is said to be saturated. If there are carbon- carbon double bonds in the molecule, this gives an unsaturated fatty acid. One structural consequence of this is that saturated fats pack closely together and tend to be solid, whereas in unsaturated fats kinks are introduced and the fatty acid chains do not fit together closely. This generally means that unsaturated fats are oils rather than hard fats. Most animal fats are saturated, those from plants tend to be unsaturated.

Some common fatty acids are shown in Table 2.2.1.

Table 2.2.1: Some common fatty acids found in lipids. Saturated fatty acids have no C=C double bonds. Oleic acid has one C=C double bond, linoleic acid has 3, and is therefore polyunsaturated.

Fatty acid No. of Saturated/ Structure carbons unsaturated

palmitic acid 16 saturated CH

(CH

)

COOH stearic acid 18 saturated CH

(CH

)

COOH

oleic acid 18 unsaturated CH

(CH

)

CH=CH(CH

)

COOH linoleic acid 18 polyunsaturated CH

(CH

CH=CH)

(CH

)

COOH

Glycerol and fatty acids are joined together by dehydration

(condensation) synthesis reactions between the hydroxyl and carboxyl groups, generating a triacylglycerol (triglyceride). This is shown in Fig.

2.2.2.

Fig. 2.2.2: Triglyceride structure. The glycerol molecule acts as the

‘backbone’ to which three fatty acids are attached by ester linkages. This gives a triacylglycerol or triglyceride. The properties of triacylglycerols are determined by the properties of the fatty acids

Phospholipids

An important variant of the triacylglycerol structure is where one of the

fatty acids is replaced by a phosphate group, which often has other

groups attached. Usually one fatty acid is saturated, and one is

unsaturated. The most abundant phospholipid in animal tisue is

phosphatidylcholine (Fig. 2.2.3).

Fig. 2.2.3: Phosphatidylcholine. This phospholipid has two fatty acid tails, one saturated (S) and one unsaturated (US). The polar head region is a choline/phosphate group linked to the glycerol backbone.

As phospholipids have a non-polar fatty acid ‘tail’ and a polar ‘head’, they are hydrophilic (water-loving) at the head and hydrophobic (water-hating) at the tail. This is a critical property in that it enables phospholipids to form bilayers, as shown in Fig. 2.2.4. As we shall see later, this is important in membrane structure.

Fig. 2.2.4: Phospholipids can form bilayers, with the polar heads on the outer (hydrophilic) surface, and the fatty acid tails forming a

hydrophobic inner region.

Steroids

These lipids have a markedly different structure to that found in the

glycerol-based triglycerides and phospholipids. Steroids are based on a

four-ring structure, with associated side chain variations. The best

known example of a steroid is cholesterol, which is found in cell

membranes. Other steroids such as testosterone are hormones. The

structure of cholesterol is shown in Fig. 2.2.5.

Fig. 2.2.5: The structure of cholesterol is based on a four-ring structure.

Not all the atoms are labelled. Testosterone and other steroid hormones are similar, with different attached groups defining their chemical properties.

2.3 Proteins

Protein molecules are heteropolymers made up of amino acids, of which there are 20 that are used in proteins. Variation in the length of the amino acid chain, and the order of the individual amino acids in it, theoretically enables an essentially unlimited variety of proteins to be constructed. This makes proteins the most diverse group of

macromolecules in the cell, with many different roles to play in both structural and functional terms.

Amino acid structure

Amino acids are characterised by the amino (HN

) group and the carboxylic acid (COOH) group. These are attached to the central or alpha carbon atom, which also carries a hydrogen atom and the variable part of the molecule (the R-group). Like carbohydrates, amino acids show isomerism, existing in both the

- and

-forms. The

-form is found exclusively in proteins. At neutral pH amino acids exist in the ionised form, although the charges on the amino and carboxylic acid groups disappear when the monomers are joined together. The simplest amino acid is glycine, which has a hydrogen atom as the R-group. A methyl (CH

) group gives alanine, shown in Fig. 2.3.1.

Fig. 2.3.1: Amino acid structure. Amino acids have a hydrogen, and

amino group and a carboxyl group attached to the central α-carbon

atom. The fourth position is a variable side-chain or R-group. In this

example the R-group is a methyl group, giving the amino acid alanine.

As the variable part of amino acid structure, it is the R-group that gives each amino acid unique chemical properties. Interactions between R- groups also specify the particular shape that the protein has, and determine its overall properties. R-groups can be classed as acidic, basic, uncharged polar, and nonpolar. Some examples of the types of side chain found in these classes are shown in Table 2.3.2.

Table 2.3.2: Types of R-group found in amino acids. The number of amino acids (total 20) in each class is shown. The three-letter and single-letter abbreviations are shown as Asp / D etc.

Class/No. amino acid abbreviation R-group amino acids

Acidic aspartic acid Asp / D -CH

COOH (ionises to COO

) (2)

glutamic acid Glu / E -CH

CH

COOH (ionises to COO

)

Basic lysine Lys / K -(CH

)

NH

(ionises to NH

) (3)

Uncharged serine Ser / S -CH

OH polar

(5) asparagine Asn / N -CH

C=O

NH

(uncharged but polar)

Nonpolar glycine Gly / G -H (10)

alanine Ala / A -CH

cysteine Cys / C -CH

SH

The peptide bond

Proteins are made by joining amino acids together by an amide linkage

called the peptide bond. A chain of amino acids is therefore known as a

polypeptide. The peptide bond is formed by a dehydration synthesis

reaction between the carboxylic acid group of one amino acid and the

amino group of the next, as shown in Fig. 2.3.3. Amino acids joined

together in this way are called residues. Although the peptide bond

itself is a planar (flat) structure which does not allow rotation around

the C-N bond, the single bonds on either side of the peptide bond do allow rotation of the residues, which makes polypeptide chains very flexible structures. This is important in determining the way in which chains of amino acids can fold to generate the highly ordered structures found in complex proteins.

Fig. 2.3.3: The peptide bond links amino acids together by a

dehydration synthesis between the carboxyl and amino groups of two different amino acid monomers. This gives the C-N linkage that is characteristic of the planar (flat) peptide bond.

Levels of protein structure

No group of biochemical molecules illustrates the concept of emergent properties better than the proteins. From the constituent atoms of the amino acids up to the final form of a large protein macromolecule, progressively more complex structural organisation enables specific form and function to be generated. To make sense of this complexity, protein chemists recognise four levels of protein structure, beginning with the sequence of amino acids in the polypeptide chain.

Chemical bonding is obviously critical in determining protein shape, and different types of bonds are important at different levels. The covalent peptide bond that links amino acid residues together is a very strong bond. In higher-order protein structure weaker interactions are

important. These involve non-covalent bonds such as hydrogen bonds and ionic bonds, van der Waals attractions, and hydrophobic

interactions where the hydrophobic parts of R-groups tend to associate

together.

Primary (1°) structure

The primary structure of a protein is the sequence of amino acid residues in the polypeptide chain. The chain of amino acids has an amino terminus at one end and a carboxyl terminus at the other, reflecting the structure of the amino acid molecules. In writing out primary structures of proteins, the convention is to write from the amino terminus (N-terminus) on the left to the carboxyl terminus (C- terminus) on the right. In some cases the structure of the amino acid residues can be shown, although mostly the abbreviated names for the amino acids (either the three-letter abbreviations or the single-letter designations) are used. Representations of primary structure are shown in Fig. 2.3.4.

Fig. 2.3.4: Primary structure of a polypeptide. This could be written out in full, but is usually abbreviated to save space. In (a) a diagrammatic representation of the polypeptide is shown, with the N- and C-termini labelled. (b) shows the three-letter abbreviations for a short peptide sequence, and (c) shows the single-letter abbreviations for the same sequence. The N- and C-terminus labels may be omitted; if so the convention is that the N-terminus is on the left.

Secondary (2°) structure

There are two main types of secondary structure. These are the αα αα-helix α and the βββββ-sheet arrangements, which are generated from interactions between the atoms of the amino acid residues in the polypeptide chain.

In the α-helix, as shown in Fig. 2.3.5, the polypeptide chain is coiled into a right-handed helix by hydrogen bonds between the N-H group of a peptide bond and the C=O group of the peptide bond four residues away from it.

In the β-sheet configuration, polypeptide chains are linked together in a

side-by-side configuration, again by hydrogen bonding. Beta sheets can

be either parallel or antiparallel, depending on the orientation of the

constituent parts of the arrangement. The two types of β-sheet are

shown in Fig. 2.3.6.

Fig. 2.3.5: The α-helix. This secondary structure is a right-handed helix with four residues per turn. Hydrogen bonds between oxygen and hydrogen atoms stabilise the helix. Not all H-bonds are shown.

Fig. 2.3.6: The β-sheet arrangement of secondary structure can be either parallel or antiparallel. In the parallel arrangement the polypeptide chains run in the same direction with respect to their N/C polarity. In the antiparallel arrangement, the chains run in opposing directions.

Hydrogen bonds are shown by dotted lines.

Tertiary (3°) structure

The α-helix and β-sheet arrangements are relatively simple ways to organise stretches of polypeptide chain. More complex structures are found when we look at the tertiary structure of proteins, which describes the way in which the polypeptide folds to give the final protein structure. Given that a polypeptide may be several hundred amino acid residues in length, and that both α-helix and β-sheet arrangements may be found in the same protein, it is easy to see that predicting and analysing protein structure is a difficult task. Modern computer graphics programmes enable scientists to look at protein structure in ways that were not possible a few years ago, and many new insights have come from computer modelling coupled with

experimental techniques such as examining protein crystals by X-ray crystallography and nuclear magnetic resonance (NMR).

The tertiary structure of a protein is determined largely by hydrophobic interactions, which place the non-polar R-groups in the centre of the molecule. In many proteins, an additional important type of covalent bond is the disulphide bond, which can form between the sulphydryl (SH) groups on cysteine residues in different parts of the polypeptide (or between cysteine residued in two different polypeptides). Within any tertiary structure, parts of the amino acid sequence may adopt an α- helix arrangement, others may be β-sheets or more complex

arrangements of the β-sheet structure. A representation of the tertiary

structure of myoglobin is shown in Fig. 2.3.7.

Fig. 2.3.7: Tertiary structure of myoglobin. This is a single polypeptide chain with several α-helices linked by non-helical regions. Folding of the protein produces a hydrophobic ‘pocket’ for the haeme group, which contains the iron atom involved in binding oxygen. This representation is a ribbon plot generated by the widely used RasMol computer software package (copyright Roger Sayle, public domain). This programme

enables the structure to be viewed in many different ways such as ball- and-stick or spacefilled, and also permits rotation of the structure to enable viewing from different angles. Software such as this is of great benefit to protein chemists.

Folded proteins may have other non-protein groups associated with them. These are called prosthetic groups, and are often essential for the biological activity of the protein. Examples include the iron-

containing haeme group of myoglobin (see Fig. 2.3.7) and haemoglobin.

Proteins may also have carbohydrate, lipid or nucleic acid groups associated with them; these conjugated proteins are known as glycoproteins, lipoproteins and nucleoproteins, respectively.

The fact that proteins are relatively stable structures in the cellular environment is remarkable in that the weak forces that hold the

structure together can be disrupted easily if the chemical environment changes, or if the sequence of the amino acids is altered. Proteins fold to give a structure with the lowest free energy, therefore each polypeptide chain will have its own preferred conformation. Thus, although in theory there are essentially unlimited possible protein structures, only a small number of these possibilities will fold to give a single stable

conformation, which has enabled the evolution of protein structures

that are stable and uniquely suited for a particular purpose.

Quaternary (4°) structure

Many proteins are made up of a single polypeptide chain, which folds to a particular tertiary structure unique to that protein. Other proteins are composed of two or more polypeptide subunits, each of which has its own specific conformation. The organisation of the subunits in a multi- subunit protein is known as the quaternary structure of the protein. A good example is the tetrameric protein haemoglobin, composed of two α- and two β-globin subunits, each with its own prosthetic haeme group.

Protein motifs and domains

As our knowledge of protein structure has improved, two additional elements have been recognised within the traditional 1°/2°/3°/4°

classification. These are motifs and domains. Motifs are elements of secondary structure that form in particular ways. Examples include the βββββ-α αα αα-βββββ motif, which gives a fold or crease in the protein, and the

βββββ-barrel, which forms a tube-like arrangement within the protein.

Domains are regions of the polypeptide chain that fold independently to give structurally distinct regions of tertiary structure, often with

different roles to play in the complete protein.

Function of proteins

As might be expected from their structural complexity and diversity, proteins have an equally wide range of different roles in the cell. One common way of describing proteins is to group them as either fibrous (structural) proteins, or globular (functional) proteins. However, this is a rather simplistic classification, and it is better to classify proteins using a more specific system that takes into account the many different and highly specific roles that they carry out. Thus we have proteins that act as enzymes, those that are found as structural components of cells and tissues, receptor and signalling proteins, and many others. Some

examples of the types of function that proteins carry out in the cell are

shown in Table 2.3.8.

Table 2.3.8: Some classes and functions of proteins in the cell.

Class of Function Examples

protein

Enzyme Catalysis (breaking & Thousands of examples! Usually forming of covalent enzyme names end in -ase. Groups bonds). include proteases, lipases,

polymerases, kinases, phosphatases, isomerases, dehydrogenases, etc.

Structural Provide support to cells Collagen, elastin, tubulin, keratin,

and tissues. actin.

Receptor Detection and Insulin receptor, acetylcholine transmission of signals. receptor, rhodopsin.

Signal Intercellular signalling. Insulin, other hormones & growth factors.

Transport Carries small molecules In the bloodstream, haemoglobin or ions in bloodstream carries oxygen, serum albumin carries or in membranes. lipids, transferrin carries iron. Many

transmembrane proteins act as pumps for transporting small molecules or ions (protons, calcium, glucose) across the membrane.

Motor Generates movement. Myosin in muscle is the most obvious example, also dynein in cilia and flagella. Kinesin interacts with microtubules to move organelles.

Storage Stores small molecules Ferretin stores iron in the liver.

or ions. Ovalbumin (egg white) and casein (milk) are storage proteins.

Regulatory Binds to DNA to regulate The lac repressor binding to the gene activity. operator of the lac operon to switch

it ‘off’.

Special Varied range of specialist Glue proteins to attach mussels to

purpose functions. rocks, antifreeze proteins of Arctic

and Antarctic fish, plus many other

specialised examples.

2.4 Nucleic acids

The information-carrying molecules of the cell are the nucleic acids DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). When compared to the complexity of proteins, nucleic acids have a relatively simple chemical structure that is based on a sugar-phosphate backbone. The variable information-coding part of nucleic acids is made up of a set of four nitrogenous bases, which arrange themselves in pairs. One of the most fascinating aspects of molecular biology is how this very simple coding system enables the great diversity of protein molecules to be constructed. As we shall see, the answer is yet again another elegant example of one of our main themes – that of emergent properties.

Nucleotide structure

The monomeric units of nucleic acids are the nucleotides. These are composed of a pentose sugar (ribose in RNA, deoxyribose in DNA) and a phosphate (PO

) group that make up the constant structural part of the molecule, and a variable nitrogenous base. The bases are either purines (double-ring structures) or pyrimidines (single-ring

structures). This difference has important consequences for the way in which the bases join together in the DNA molecule. The purine bases are adenine and guanine (A and G, found in DNA and RNA). The pyrimidines are cytosine (C, DNA and RNA), thymine (T, DNA only) and uracil (U, found in RNA instead of thymine). Nucleotide structure is shown in Fig. 2.4.1.

Fig. 2.4.1: Nucleotide structure. This is based around a 5-carbon sugar

(shaded) with a phosphate and a nitrogenous base attached to the C5

and C1 positions respectively. In RNA the sugar is ribose, with an OH

group at position X on C2. In DNA the sugar is deoxyribose, with X being

a hydrogen.