Eureka: Physiology, second edition

By Jake Mann and David Marples

Eureka: Physiology 2e provides everything a student needs to succeed in the subject, prepare for their clinical placements and pass their exams.

Logical book structure to aid the learning process:

• The book starts with a First principles chapter which clearly explains key concepts and the mechanisms of physiology.
• The subsequent systems-based chapters, including neuromuscular, cardiovascular, respiratory, renal, endocrine, and gastrointestinal systems, describe the physiological processes which underpin normal function.
• The book concludes with a final Applied physiology chapter showing how the body responds to stress, exercise, high altitude and massive blood loss.

Key features, to help learn the subject and link it to real world medicine:

• an engaging and authoritative style – with everything you need in one place
• realistic clinical cases – these show how skilled clinicians work through a presentation, and put disease and biomedical principles into context
• extensive range of photographs – superb photos show clinical presentations and exactly how to demonstrate related clinical signs
• starter questions – stimulating questions and answers to test your knowledge and highlight the level of detail you need
• study boxes – these highlight tips, tricks and key learning points

Featuring insightful clinical cases, extensive illustrations and photographs, self-assessment questions and answers, and a wealth of other learning tools, Eureka: Physiology 2e will equip you with the core knowledge and skills you need for your exams and clinical placements!

• Language: English
• Publisher: Scion Publishing
• Release date: Oct 17, 2022
• ISBN: 9781914961236

Book preview

Chapter 1

First principles

Starter questions

What is the central dogma of molecular biology and genetics?

If DNA comprises a sugar, phosphate and a base, why is it an acid?

Why is it thought that mitochondria were once separate organisms?

How do cells keep a different apical and basal membrane?

How does fish oil interfere with arachidonic acid signalling?

Why is it difficult to utilise adult stem cells to grow organs?

Answers to questions are to be found in Section 1.9.

1.1Introduction

Genetic material codes for the production of proteins, which go on to assemble the machinery and structures of cells. These cells associate with each other to form tissues, and multiple tissues interact and combine to form organs. Thus the body has layers of complexity that, in principle, can ultimately be reduced to cells and the molecules they contain. Human physiology – the normal functions and interactions of human tissues – is described in terms of cells and molecular reactions.

1.2Levels of organisation

1.2.1Cellular theory of life

Cells are membrane-bound units capable of self-replication. All living things are composed of cells, from humans, with about 10 trillion cells, to single-celled organisms such as amoebas.

Organisms are divided into two groups:

Eukaryotes, which sequester their genetic material (DNA) within a membrane-bound structure (the nucleus) inside the cell

Prokaryotes, which do not have a nucleus separating their DNA from the rest of the cell.

Table 1.1Differences between eukaryotic and prokaryotic cells

There are a number of differences between the two (Table 1.1).

Mammals are eukaryotic organisms with a huge diversity of cell types, each specialised for a particular function. When cells with a particular function are grouped together, a tissue is formed. This is the basis for how the human body functions (Figure 1.1).

Figure 1.1Organisms, systems, organs, tissues and cells are composed of atoms and the reactions between them.

1.2.2Macromolecules

Four elements comprise the majority of every biomolecule: oxygen, carbon, hydrogen and nitrogen. A large number of other elements (e.g. iron, magnesium, selenium and copper) are present in the human body in smaller amounts.

Biomolecules range from very small molecules such as metabolic intermediates (e.g. cyclic AMP) to large macromolecules such as proteins, lipids, carbohydrates and nucleic acids). Large macromolecules are formed by the assembly of smaller molecules that undergo activation to allow the formation of bonds. The principal macromolecules are:

Proteins

Lipids

Carbohydrates and

Nucleic acids.

Proteins

Proteins are a diverse group of macromolecules with a range of functions (Table 1.2). Many are enzymes, proteins that control many of the body’s processes, including production of the other macromolecules.

Table 1.2Types of protein, grouped by function

Each protein is composed of a number of amino acids, small molecules that each contain an amine group (–NH

2

) and a carboxylic acid group (–COOH). These give proteins the ‘N-terminus’ and ‘C-terminus’, respectively, when the chain of amino acids is bound together. Peptide bonds form between the amine group of one amino acid and the carboxylic acid group of the next amino acid, to form chains called peptides (short chains of 2–4 amino acids) or polypeptides (longer chains). Each peptide folds into complex three-dimensional structures (Figure 1.2). In this way, there are four ‘levels’ of protein structure, summarised in Table 1.3. Some proteins comprise a single polypeptide chain and therefore have no quaternary structure.

Figure 1.2The amino acid sequence of a protein is its primary structure; this ultimately determines its secondary (α-helix or β-pleated sheet) and tertiary structure.

Table 1.3The four levels of protein structure

There are hundreds of amino acids but only 22 are used by the body to make proteins. Four of them are made by the body (non-essential amino acids): alanine, asparagine, aspartic acid and glutamic acid. The rest are obtained from the diet and are termed ‘essential’ amino acids because the diet must contain enough of each to maintain health.

Lipids

A fatty acid comprises a long hydrocarbon chain that ends with a carboxyl group; the hydrocarbon chain is insoluble in water, but the carboxyl group is water-soluble. A phospholipid ends in a charged phosphate group instead of a carboxyl group. These are the archetypal amphipathic molecules: containing a hydrophobic region (hydrocarbon tail) and hydrophilic region (phosphate head).

Diglycerides are formed of several lipids united by a glycerol group: diglycerides comprise two fatty acids plus a glycerol group; triglycerides comprise three hydrocarbon chains plus a glycerol group. Other lipids, such as cholesterol, have several carbon rings. The carbon rings in cholesterol are important for interrupting the bonds between adjacent hydrocarbon chains in phospholipid membranes. The principal roles of lipids are as:

the main component of cell and organelle membranes (see Section 1.4.1)

amphipathic molecules at the body’s water interfaces, due to the hydrophobic nature of lipids (e.g. pulmonary surfactant, bile acids)

high-energy storage molecules

intracellular signalling molecules.

Carbohydrates

Simple sugars (monosaccharides) are linked together by glycosidic bonds to form polysaccharides, also called carbohydrates. These act as energy sources, structural molecules, signalling molecules and are a major component of nucleic acid.

Nucleic acids

A nucleic acid is a macromolecule composed of a sugar and phosphate backbone and nitrogenous bases (also called nucleobases). Their structure is described in detail in Section 1.3.3. The most abundant nucleic acids in human cells are deoxyribose nucleic acids, referred to as deoxyribonucleic acid (DNA), and ribose nucleic acids, referred to as ribonucleic acid (RNA). These form the genetic material that controls all cell processes and allows conservative replication of living organisms, i.e. formation of a new, daughter organism using the nucleic acid template of the parent organism.

Mucopolysaccharidosis is a rare disease involving abnormal storage of macromolecules, in this case, glycosaminoglycans (a form of polysaccharide). It is caused by a dysfunctional mutation of a catabolic enzyme and causes liver and heart failure.

1.3The cell

1.3.1Cell structure

Human cells are 10–100 μm structures bound by a phospholipid membrane. They contain an aqueous solution of chemicals, the cytosol. Lying within the cytosol are smaller, membrane-bound, functional units called organelles, each with their own specific role (Figure 1.3). Together, the cytosol and organelles are referred to as cytoplasm.

Figure 1.3General cell structure. This generic cell shows multiple organelles that are not necessarily present in all cells. Most human cells have specialisations related to their function.

1.3.2Cytosol

Most of the cell’s volume is cytosol, and over 80% of this is water. It also contains dissolved ions, signalling molecules, reaction substrates and macromolecules. However, only a minority of cell reactions occur in the cytosol itself, glycolysis being a major example; the majority occur on the surfaces of membranes.

1.3.3Nucleus

The nucleus is the location of the cell’s genetic material, its DNA, which controls the cellular processes. It is bounded by a double membrane with perforations to allow passage of macromolecules to and from the cytosol. As well as DNA, it contains nucleoli, which are condensed areas of RNA and protein and are the location of ribosome synthesis.

The essence of nuclear (and cellular) function is that DNA is used to make RNA, which then is used as a code to follow in constructing proteins. The process is controlled at multiple levels, especially during the transcription (copying) of DNA into RNA (Figure 1.4), which is the first step in moving from a permanent copy of genetic material (the DNA) to a temporary form (RNA). A further key feature of DNA is that it is replicated and transmitted through successive generations of cells. Together these are said to be the ‘central dogma’ of molecular biology and genetics.

Figure 1.4The central dogma of molecular biology and genetics: replication of DNA, transcription of DNA and translation of RNA.

Structure of DNA

DNA is made of two helical strands of nucleotides. Each nucleotide is formed from a deoxyribose sugar group, a phosphate and a nitrogenous base. The sugar and phosphate groups form the backbone of the strand, and the bases hang off the strand like the charms on a bracelet. There are four different bases, divided into two groups:

pyrimidines: cytosine (C) and thymine (T)

purines: adenine (A) and guanine (G).

In DNA, two strands are held together by hydrogen bonds between the bases. These bonds are formed only within two specific pairings: thymine–adenine and cytosine–guanine (Figure 1.5). Other pairings are not possible; for example, cytosine does not pair with adenine. In this way, each strand is like a mirror image of its partner, which is an essential characteristic for replication (see below). Note that a purine always pairs with a pyrimidine.

Figure 1.5The two anti-parallel strands of DNA comprise its molecular structure. These entwine to form a helix, which must be opened or unwound to allow access to the DNA.

The two ends of a DNA strand are different: one terminates in a phosphate group and is called the 5ʹ end; the other terminates in a hydroxyl group and is called the 3ʹ end. DNA strands have polarity, a ‘direction’, because new DNA is always synthesised in the 5ʹ-to-3ʹ direction. The polarity refers to the carbon atom in the ribose sugar on the free end of the DNA strand. The two DNA strands are anti-parallel: one strand is 5ʹ-to-3ʹ, the other is 3ʹ-to-5ʹ.

Folding of DNA

The helical strands of DNA are packaged with a number of proteins in a form termed chromatin. The DNA is wrapped around small complexes of histone proteins (Figure 1.6) to form a nucleosome, with about 200 base pairs to each nucleosome. On high-power electron microscopy the nucleosomes look like beads on a string. There are then further levels of coiling and winding to produce densely packed chromosomes formed of chromatin.

Figure 1.6The DNA helix is wrapped around histone proteins, forming nucleosomes, in a ‘beads on a string’ appearance. It is further condensed to give chromosomes formed of chromatin.

This tightly packed inactive DNA, not undergoing replication or transcription, is termed heterochromatin. Active DNA is relatively unwound, as euchromatin.

At the end of chromosomes are telomeres, which are repetitive sections of DNA that shorten with cell division. This DNA does not code for proteins but does allow DNA replication machinery to go right to the end of the coding DNA (this is a particular problem for the lagging strand, as described below). Telomeres normally shorten with age, which promotes cellular senescence and, in some cases, malignant transformation. However, telomeres do not shorten as much as would be expected because they are made by the enzyme telomerase, which uses an RNA template to protect their integrity. Humans with (very rare) mutations in telomerase have early-onset fibrotic disease in the lung and their bone marrow may stop producing blood cells. Cancer cells, on the other hand, have high telomerase activity and this may help them continue to divide without become senescent.

Replication of DNA

The ability of DNA to be replicated exactly is fundamental to tissue function. Replication is called semi-conservative because the parent DNA is split in half, with each strand ‘directing’ the formation of a new daughter strand. Because there are only two possible pairings of the bases in DNA, the resultant pairs of strands are exact copies of the original parents, for example:

DNA replication is extremely accurate but occasional errors do occur. Mismatch repair proteins – for example, mutation S and L homologous (MSH and MLH, respectively) proteins – help identify base-pairing errors. Lynch syndrome is a hereditary disease of increased risk of non-polyposis colorectal cancer due to mutations in MSH-2 and MLH-3.

The enzyme DNA helicase opens up the helix at a point called the replication fork, which is stabilised by topoisomerase, i.e. closure of the separated strands is prevented and DNA is kept relatively unwound (Figure 1.7). A new strand is synthesised in a 5ʹ-to-3ʹ direction on the leading strand as DNA polymerase moves along the parent 3ʹ-to-5ʹ strand. This enzyme uses new nucleotides to match corresponding base pairs. It does this with high accuracy. In addition there are a number of other mechanisms that check for and repair errors during replication.

Figure 1.7In semi-conservative replication of DNA there is formation of two new DNA strands, with half of each strand consisting of half of the parent strand.

The daughter formed on the other (‘lagging’) strand is made in a 3ʹ-to-5ʹ direction and is formed in small sections known as Okazaki fragments, made by DNA polymerase moving in the 5ʹ-to-3ʹ direction. Each fragment is begun with an RNA primer (made by an RNA polymerase termed ‘primase’), which allows DNA polymerase to add subsequent bases. The Okazaki fragments are joined together by DNA ligase. The RNA primer is cleared from DNA and recycled.

DNA repair and editing

There are multiple endogenous systems in place for correcting errors in DNA generated during replication or in response to oxidative stress and radiation. These include the BRCA1/2 genes and mismatch repair system (e.g. MSH2), where loss predisposes to early-onset cancer.

The ability to ‘edit’ DNA is also of major interest in scientific research and the simplest system is known as CRISPR-Cas9. Cas9 is a DNA nuclease (an enzyme that cuts DNA) when it is guided into place by a guide RNA specific for a region of DNA. When Cas9 and the guide RNA bind to the target region, the DNA is cut; this then allows for a new template of DNA to be provided and inserted to edit that region (e.g. correct a mutation). This system originally evolved as a way that bacteria could defend themselves against viruses by destroying the viral DNA, but it is now a major tool in molecular biology and may help in the treatment of genetic diseases.

1.3.4From DNA to RNA to protein

A gene is a section of DNA that contains a code for the production of a single protein, first by transcription to produce an RNA transcript, and then by translation of the RNA into an amino acid chain, i.e. a polypeptide or protein. This type of RNA is called messenger RNA (mRNA) because it acts as a messenger between the gene and the cellular mechanism that builds proteins.

In a typical eukaryotic gene several stretches of DNA called exons code for the protein; these are interrupted by regions called introns. The introns are removed from (‘spliced’ out of) the RNA transcript before it is translated into a polypeptide. Some genes undergo alternative splicing, where different exons end up in the mRNA, thus resulting in a group of related protein products called splice variants.

Transcription

The first step in the formation of a protein is transcription (Figure 1.8): this is the process of turning a gene (DNA) into an mRNA template. Only one strand of the double-stranded DNA is copied and the product is a single-stranded mRNA molecule that detaches from the DNA. There are four stages:

Initiation: a complex of transcription factors and proteins bind to a promoter region of DNA ‘upstream’ of the gene (i.e. towards its 5ʹ end). The transcription factor complex causes separation of DNA strands and guides RNA polymerase to the site of the gene. RNA polymerase is guided into place by the TATA box, a region of DNA of alternating thymine and adenine bases.

Elongation: RNA polymerase II binds to the DNA and catalyses formation of a single-stranded mRNA chain that is complementary to the DNA (there are several RNA polymerases but only RNA polymerase II forms mRNA). The nucleotides used to synthesise the (m)RNA contain ribose sugar groups instead of deoxyribose sugars and include uracil instead of thymine.

Termination: specific codes and repetitive sequences in the DNA result in dissociation of RNA polymerase from DNA when copying has reached the end of the gene, and transcription ends.

Post-transcriptional modification: the mRNA initially formed (pre-mRNA) undergoes a series of modifications in the nucleus, as outlined in Table 1.4, before it is translated into protein.

Figure 1.8DNA is unwound and opened to allow transcription to take place. Pre-mRNA, a single-stranded molecule, is formed and then is moved from the nucleus to the cytosol.

Table 1.4Processing of pre-mRNA prior to translation

Translation

In translation amino acids are matched to codons on the mRNA, and the amino acids are joined together in sequence to form a protein.

A codon is a trinucleotide. Each of the 22 amino acids has one or more RNA codons that correspond only to that amino acid. For example, AUG is one codon for the amino acid methionine and GGA is one codon for glycine. The matching of amino acids to codons is performed by transfer RNAs (tRNAs). At one end of each tRNA molecule there is an anticodon, a trinucleotide that binds to a specific codon; at the other end there is a binding site for the corresponding amino acid. The first codon in all proteins is AUG, encoding methionine, therefore AUG is known as the ‘start’ codon.

Translation is mediated by ribosomes, specialist RNA and protein complexes (Figure 1.9). The ribosome binds to, and moves along the mRNA. As it does this it reveals each codon in sequence, and facilitates binding of the corresponding tRNA, thereby bringing into line the sequence of amino acids determined by the codon sequence of the mRNA. The ribosome catalyses the formation of peptide bonds between the adjacent amino acids, generating the polypeptide chain. This continues until a ‘stop codon’ (e.g. UAG) is reached; there is no corresponding tRNA for this codon (and no amino acid), and translation ends.

Figure 1.9Translation of RNA is mediated by ribosomes. Each ribosome has two binding sites for tRNA. When a tRNA anti-codon binds the mRNA codon, a peptide bond can form between the amino acids attached to that tRNA and the adjacent tRNA.

There tends to be only one ribosome translating upon each mRNA at any one time; however, ribosomes are short-lived structures that may not even translate an entire mRNA molecule; they undergo frequent recycling. Occasionally several ribosomes join together as a polysome on a single mRNA, each ribosome translating it at the same time; this allows for formation of multiple polypeptide chains simultaneously.

Regulation of protein production

Cells produce some proteins constitutively, i.e. at a constant rate, whereas others are inducible, i.e. they are only produced in response to specific signals. Control for these processes exists both before and after transcription.

For example, in response to growth factor stimulation there is activation of a tyrosine-kinase pathway called the Ras-kinase pathway, which results in generation of the Fos and Jun family of transcription factors. These transcription factors bind to promoter regions on DNA; these regions are associated with growth-related genes. Binding of the transcription factors promotes assembly of the TATA-box binding complex (TBBC), which recognises a T-A-T-A section of DNA downstream from the promoter region but upstream from the gene. Assembly of the TBBC guides RNA polymerase II to the site of the gene and increases transcription.

Another form of regulation is degradation and post-transcriptional modification of mRNA to reduce gene translation. A further mechanism that is still poorly understood is performed by microRNAs (miRNAs). These are small RNAs that are able to bind to and interfere with the function of mRNAs in a sequence-specific manner.

RNA can be degraded by RNA interferences, through assembly of the RNA-induced silencing complex (RISC). This is a complex of proteins that includes Argonaute, which is an RNase that cleaves RNA (thereby degrading it). RISC needs an RNA template to help recognise specific mRNAs and this template can come from endogenous microRNAs or through exogenously supplied small interfering RNA (siRNA). Both siRNA and miRNA are first processed by another enzyme called Dicer, which cleaves miRNA or siRNA into short double-stranded RNA sections, that acts as the template for RISC.

This is a highly conserved process that has evolved as part of the response against viral infections. siRNA is now a major tool in scientific research for ‘gene silencing’ and there are several siRNA drugs licensed for treatment in humans.

Oncogenes are normal genes that promote growth or cell survival (e.g. growth factors and anti-apoptotic factors). In carcinogenesis, mutations occur in oncogenes, disrupting normal regulation of gene production and culminating in increased synthesis of growth-related proteins and cell proliferation.

1.3.5Mitochondria and energy production

Mitochondria

The mitochondrion is a structure that has its own double membrane, separating it from the rest of the cell, and its own DNA. Mitochondria are thought to have originated as separate organisms that developed a symbiotic relationship with early eukaryotic cells. They are the sites of oxidative phosphorylation and generation of ATP (adenosine triphosphate), the final stage in aerobic respiration where all pathways of energy generation converge (Figure 1.10). Thus mitochondria are often described as the powerhouses of the cell and are more abundant in cells with high-energy demands, e.g. skeletal muscle cells.

Figure 1.10Outline of human metabolism showing energy generation from the three main macromolecules: protein, carbohydrate and fat. All converge on the Krebs cycle (i.e. the TCA cycle or citric acid cycle) for oxidative phosphorylation.

Mitochondria contain their own (small) genome coding for proteins involved in their function. Rare inherited conditions caused by mutations in mitochondrial DNA usually affect tissues with high energy demand, such as brain, muscle and eyes, e.g. MELAS (myoclonic epilepsy, lactic acidosis and stroke-like episodes). Mitochondrial DNA is inherited exclusively from the mother’s ovum.

Overview of energy production

The cellular ‘currency’ for energy exists in the form of adenosine triphosphate (ATP). ATP is able to act as an energy store because when it is hydrolysed to ADP and phosphate (P

i

) there is release of energy that drives other reactions, for example conformational change of a membrane channel for active transport (see Section 1.4.3). Therefore, the aim of energy production is to generate ATP. This is the main function of macronutrients: carbohydrates, fats and, to a certain extent, protein.

Glycolysis

Many carbohydrates are broken down to glucose, the starting molecule for glycolysis. The overall function of glycolysis is to convert glucose into pyruvate and generate two molecules of ATP. This process occurs independent of oxygen; therefore, in the absence of adequate oxygen, anaerobic respiration relies on ATP production from glycolysis alone.

Pyruvate is converted to acetyl CoA (co-enzyme A) in one of the main rate-determining steps in metabolism, regulated by pyruvate dehydrogenase. This is also the point where energy from fat, protein or fructose enters the pathway for energy generation. Acetyl CoA is the breakdown product of fat, protein and fructose, so is an intermediate between macromolecules and the tricarboxylic acid cycle (see below).

Fat and protein metabolism

Fats are broken down by β-oxidation, a process of multiple oxidation reactions that occurs within the mitochondria. Protein is stripped of its nitrogen and then converted to pyruvate.

Tricarboxylic acid cycle

Acetyl CoA is the initial molecule in the tricarboxylic acid cycle (TCA cycle, citric acid cycle or Krebs cycle). The TCA cycle takes place inside mitochondria (Figure 1.11). It is a series of reactions that result in the generation of reduced dinucleotide intermediates: nicotinamide adenine dinucleotide (

NAD

+

) is converted to NADH (the reduced form of

NAD

+

) and flavin adenine dinucleotide (FAD) is converted to FADH

2

(the reduced form of FAD).

Figure 1.11Energy production in mitochondria. Glycolysis and β-oxidation of fat supply acetyl CoA to the TCA cycle inside mitochondria. The NADH and FADH

2

that are generated by this drive the electron transport chain, which provides a hydrogen ion gradient which ATP synthase uses (on the inner mitochondrial membrane), to make ATP.

Electron transport chain

The formation of NADH and FADH

2

is a crucial step in ATP generation. These molecules donate

H

+

to protein complexes on the inner mitochondrial membrane, in a process called the electron transport chain, which pumps

H

+

to the inter-membrane space. Oxygen is required for the final stage of the ETC and is reduced to

H

2

O.

The resulting

H

+

gradient across the inner mitochondrial membrane drives ATP synthase, an enzyme that uses the passage of

H

+

through its transporter domain to allow combination of

ADP

+

P

i

to ATP. This form of ATP synthesis is known as oxidative phosphorylation; it is the most efficient method of energy production.

Mitochondrial dysfunction can arise from congenital genetic conditions, acute toxicity or chronic dysfunction. In iron poisoning, alterations in the balance of oxidation reactions within mitochondria cause cell death and liver failure. Chronic changes in mitochondrial β-oxidation of fat contribute to the inflammation seen in fatty liver disease.

1.3.6Endoplasmic reticulum and Golgi apparatus

The endoplasmic reticulum is a series of interconnecting membrane laminae (sheets) and tubules that are the location of the synthesis and modification of many molecules.

Rough endoplasmic reticulum

Rough endoplasmic reticulum (RER) is covered with ribosomes, which dock to a protein complex called the translocon. The translocon is a group of proteins in the membrane of the RER that is used to transport polypeptides into the endoplasmic reticulum once they have been synthesised by ribosomes. Some ribosomes are free floating in the cytosol and then bind to the translocon, if they have a corresponding amino acid sequence in the synthesised polypeptide.

The main role of the RER is the production of secretory and intrinsic proteins. The proteins are synthesised by ribosomes and pass through the translocon into either the lumen or the membrane of the RER. Some proteins undergo post-translational modifications inside the RER, such as glycosylation, cleavage or adenylation, prior to being fully functional; enzymes in the RER mediate this.

Smooth endoplasmic reticulum

Smooth endoplasmic reticulum (SER) has several functions. It is the site of synthesis of steroid hormones in endocrine cells (e.g. in the cortex of the adrenal gland). It is a store for calcium, which is released as a ‘second messenger’, i.e. an intracellular signal (see Section 1.5.3). In its membranes, SER also has specialised calcium release channels that open in response to other second messenger signals such as inositol trisphosphate (IP

3

).

The SER in muscle cells is specialised, and is known as the sarcoplasmic reticulum. It contains very high

Ca

²+

concentrations due to active uptake via a SERCA pump (sarcoplasmic reticulum calcium-transporting ATPase, an active calcium transporter).

Golgi apparatus

The Golgi apparatus consists of a stack of plate-like cisternae that are flattened balloons of membrane. Material enters the Golgi by endocytosis, travels between cisternae and departs for other regions of the cell, all by vesicular trafficking. After proteins (or large lipids) have been synthesised in the endoplasmic reticulum, they pass into the cis-Golgi network. Enzymes within the cisternae modify the proteins (for example by glycosylating them), and sort and package them for particular cellular targets. Secretory vesicles bud off the trans-Golgi network and travel towards the surface membrane of the cell before exocytosis, i.e. discharge out of the cell (Figure 1.12).

Figure 1.12The Golgi apparatus has a cis face that receives proteins from the endoplasmic reticulum. The trans face produces secretory vesicles that travel to the cell surface membrane.

1.3.7Other cellular structures and specialisations

Cytoskeleton

Cells contain three networks of fibres that maintain the shape of the cell and provide a substrate for intracellular transport.

Microfilaments

These are composed of actin and are particularly prominent near the periphery of cells. They form the core of microvilli and the pseudopodia of motile cells. They often anchor membrane proteins in particular domains and help cells attach to other body components.

Microtubules

These are composed of tubulin molecules. They are polar with a ‘minus’ end usually anchored in an area of cytosol that acts as an organising centre (see below), and a growing ‘plus’ end. Typically the plus ends radiate towards the periphery of the cell, though in epithelial cells they are often in an ‘apical-to-basal’ orientation. (The apical membrane of an epithelial cell faces outwards, for example towards the gastrointestinal lumen; the basal, or basolateral, membrane faces towards the basal membrane, underlying capillaries, or further layers of epithelial cells.) The microtubule network is quite dynamic and has a major role in organising the distribution of other cellular components within the cell. Microtubules are particularly important in cell division (see Section 1.3.8) when they are required for formation of the mitotic spindle and therefore are needed for progression through metaphase.

There are several cytoskeletal motor proteins that drive vesicle movement along microtubules and microfilaments (Table 1.5).

Table 1.5Cytoskeletal motor proteins and their function

The intermediate filaments

These have a mainly structural role. Different cell types have intermediate filaments made up of different proteins; for example, epithelial cell intermediate filaments are made of keratins.

Centrioles

The centrioles are a pair of small structures made up of microtubule triplets (usually 9 triplets arranged as a short hollow cylinder). During much of the cell cycle they appear quiescent, though they form the core of the microtubule organising centre. However, during cell division (mitosis) they are responsible for production of the mitotic spindle, a network of filaments that is needed for separation of the chromosomes and for cytokinesis (see Section 1.3.8).

Lysosomes

These vacuoles contain many hydrolytic enzymes, which are used for a variety of processes. For example, in granulocytes, lysosomes are used to produce toxic radicals (e.g.

O

2

–

) that kill bacteria. In thyroid follicular cells, lysosomal enzymes are used to cleave thyroglobulin into thyroxine and tri-iodothyronine. More generally, they degrade any proteinaceous material that needs to be removed from the cell.

Lysosomes fuse with autophagosomes (specialised double-layered vesicles) to make autolysosomes. These engulf cellular debris (e.g. proteins, lipid droplets) and effete organelles (e.g. mitochondria) to recycle them by the process known as autophagy. Autophagy is activated by a variety of stimuli (starvation, hypoxia, ER stress) and is believed to be a normal physiological process. A failure of autophagy is thought to lead to accumulation of damaged proteins and organelles that may promote degenerative (e.g. Alzheimer’s) and malignant disease.

Peroxisomes

These are small vacuoles that contain enzymes needed for β-oxidation breakdown of very-long-chain fatty acids.

Motile cilia

These are thin projections from the apical membrane of some epithelial cells, for example into the bronchial airways. They drive movement of material over the surface of the cells. They are formed of an axoneme, a microtubule-based cytoskeleton, covered in plasma membrane. They beat rhythmically to assist movement of mucus in the respiratory system and flow through the fallopian tubes.

Microvilli

These are multiple small fingers of the apical plasma membrane, with a core of microfilaments. Microvilli are a feature of absorptive epithelia because they greatly increase a cell’s surface area. The basolateral membrane does not contain microvilli, but may have deep folds to increase surface area.

1.3.8Cell cycle

The normal life cycle of a cell’s quiescence, growth and division is termed the cell cycle (Figure 1.13). Mitosis, the process of division into daughter cells, represents only a very small fraction of the cell cycle, so in any one tissue relatively few cells are actively dividing at any one time. The duration of the cell cycle varies greatly between cell types. For example, intestinal epithelium renews itself every 3 days whereas the majority of cardiac muscle cells (myocytes) never divide.

Figure 1.13For much of the cell cycle, the cell is in interphase (G0, G1, S, G2), with mitosis (M) comprising only a minority of the time. Checkpoints must be passed to allow cycle progression.

Most cardiac myocytes never divide, only doing so under certain conditions, e.g. after sublethal ischaemic injury followed by rapid reperfusion. Most of the (minimal) production of new cardiac myocytes occurs from stem cells residing within the myocardium.

The cycle is divided into five phases:

G0 – a quiescent phase without growth, replication or division. This phase has a highly variable duration and is when most normal cell processes take place

G1 – the first phase of growth, with an increase in cytoplasm and organelle numbers

S – synthesis of new set of DNA, by replication (as described above). This converts each chromosome from a single chromatid into two chromatids; the resulting chromosome appears as two strands, joined by a centromere at the centre; see Figure 1.14.

G2 – a further growth phase

M – mitosis phase, with division of the cell into two daughter cells.

Figure 1.14For most of the cell cycle chromosomes are formed of one chromatid, but after DNA replication chromosomes are composed of two sister chromatids joined at the centromere. Maternal and paternal copies of the same chromosome are known as homologous chromosomes.

Mitosis

This is the process of symmetrical cell division into two identical daughter cells, each containing a complete set of genetic material (two copies of each of the 23 chromosomes). The term ‘n’ is used to describe the amount of genetic material; a full set (i.e. two copies of each of the 23 chromosomes) is 2n. Therefore n is one set of 23 chromosomes. Replication occurs in the S phase, before mitosis begins; therefore at the start of mitosis, cells have 4n DNA and chromosomes are composed of sister chromatids (two exact copies of each chromosome, joined by the centromere). Mitosis is divided into four phases (Figure 1.15):

Prophase: condensation of the chromosomes, breakdown of the nuclear membrane and synthesis of the mitotic spindle (using microtubules).

Metaphase: aligning of sister chromatids on the mitotic spindle (with crossing-over of chromosome sections for exchange of alleles between chromosomes in meiosis).

Anaphase: separation of chromatids as the spindle contracts, pulling one chromatid towards each pole of the cell, with separation through the centromere.

Telophase: cytokinesis, i.e. division, of the cell into two, and re-formation of the nuclear membrane and re-establishment of normal cell function.

Figure 1.15Mitosis is divided into prophase, metaphase, anaphase and telophase (which includes cytokinesis).

Cell cycle regulation

The cell cycle is carefully controlled. Excessive cycling results in aberrant growth and proliferation of cells (neoplasia), while a lack of cycling causes atrophy (wasting). There are several checkpoints throughout the cell cycle, each requiring a specific signal to allow continued cycling. These signals result in a rise in cyclin proteins, which control progression through the cycle by activating cyclin-dependent kinases (CDK) that phosphorylate the proteins required for the cycle to continue. Mutation in the proteins that control the cell cycle checkpoints results