CHAPTER 1
Water and life
BASIC CONCEPTS:
Water makes up approximately 60% of the human body. Its molecular structure allows it to act as a solvent for many of the other key molecules which enable cells to function and life to be maintained. An understanding of the distribution of water in the body, the composition of the various fluid compartments and the control of the movement of water between compartments is crucial to understanding many basic life processes.
1.1 The properties of water
Water is essential for life. The cells of living organisms are composed of around 70% water and many of the reactions essential to life occur in an aqueous environment. The chemical properties of water make it a particularly suitable medium for supporting life. Water is a polar molecule, which is to say it has an uneven distribution of charge (Fig. 1.1).
This means that it is able to interact with other polar and charged groups. Molecules or groups that interact with water are described as hydrophilic, whereas non-polar groups are described as hydrophobic.
Virtually all the molecules of life are based around the element carbon. These include:
• sugars and polysaccharides
• amino acids and proteins
• nucleotides and nucleic acids
• lipids
Polysaccharides, proteins and nucleic acids are very large molecules, termed macromolecules, and are polymers of sugars, amino acids and nucleotides respectively. Biological macromolecules contain both hydrophilic groups (such as OH, NH2 and COOH) and hydrophobic groups (for example hydrocarbons) and the relative amounts of these influence solubility (for further information see Section 3.7 in Catch Up Chemistry).
Interactions with water play an important part in determining the structure of these biological molecules. Generally speaking, hydrophilic groups tend to be exposed on the surface of a molecule or structure from where they are able to interact with water molecules. In contrast, hydrophobic groups tend to orientate themselves towards the inside of the molecule or structure where they interact with each other forming hydrophobic bonds. Interactions between hydrophobic chains of fatty acids allow the formation of cell membranes (see Chapter 4). Other molecules that are associated with membranes, such as proteins, often have hydrophobic regions which are inserted into the membrane to form an anchor.
Water is also very important as a medium of transport and forms the basis of blood. Gases dissolve in water, and this is important in allowing oxygen to be taken to cells and carbon dioxide to be removed.
1.2 Water in the human body
Approximately 60% of the weight of the human body is water – thus a 60 kg person will contain approximately 36 litres of water. Within the body the water is distributed between three main compartments. The bulk of body water (65%) is contained in the cytoplasm of cells and is known as intracellular fluid. Most of the remaining extracellular fluid is divided into the interstitial fluid (25%) which bathes the cells and the plasma (7.5%) which is contained within the blood vessels of the circulatory system. The remaining 2.5% of fluid is known as transcellular fluid and includes, for example, the water in the bladder and the contents of the gastrointestinal tract.
Intracellular fluid is separated from interstitial fluid by the plasma membrane of the cell (see Chapter 6). The ionic composition of these two compartments is dramatically different. The extracellular fluid has a similar composition to seawater and contains approximately 140 mmol Na+ and 110 mmol Cl-. Extracellular fluid also contains significant levels of bicarbonate ions. By contrast, intracellular fluid contains high levels of K+ (approximately 160 mmol compared with 4 mmol in extracellular fluid) and low levels of Na+ (10 mmol). The intracellular negative charge is provided not by Cl- but by proteins, bicarbonate and phosphate ions.
The concentration gradients of Na+ and K+ across cell membranes form the basis of many physiological processes (see Chapters 9 and 22). Ions contained within body fluids are known as electrolytes.
A general rule which applies when considering the ionic balance of any one compartment is that it should contain equivalent positive and negative charges (determined by the relative numbers of cations and anions). Each compartment is said to be electroneutral. This has significance when considering the movement of ions across membranes because, wherever possible, the body strives to ensure that movement of positively charged cations is accompanied by an equivalent negative charge in anions. When this does not happen electrical potentials are generated across membranes and this forms the basis of the function of excitable tissues (see Chapter 16).
The two components of extracellular fluid are separated from each other by the capillary wall. In most capillaries this is freely permeable to the movement of ions and small organic molecules but does not allow the passage of proteins. Thus under normal circumstances interstitial fluid contains no protein whereas both plasma and intracellular fluid are protein rich.
1.3 Test yourself
The answers are given on p. 175.
Question 1.1
Where in a biological macromolecule would hydrophobic groups generally be found?
Question 1.2
What are the three main compartments in which body water is distributed?
Question 1.3
What is the main cation of: (a) extracellular fluid; (b) intracellular fluid?
Question 1.4
Organic molecules are based around which element?
Question 1.5
Which key component of plasma does not normally pass across the capillary wall?
CHAPTER 2
Proteins
BASIC CONCEPTS:
Proteins are macromolecules assembled as a sequence of amino acids. There are twenty different amino acids, giving rise to a wide range of possible proteins. According to the particular amino acid sequence, proteins will adopt different three-dimensional structures. Proteins are present in all cells and can perform many roles, including as structural elements and as enzymes. It is important to understand how the amino acid sequence of proteins can determine the properties of different proteins, and also how these properties can be altered by external factors such as the binding of another molecule or the addition of a phosphate group.
2.1 Introduction
Proteins are a highly diverse and important group of molecules, central to life. Proteins are biological macromolecules and are polymers of amino acids.
Amino acids contain an amino group and a carboxylic acid group (Fig. 2.1), both attached to an alpha carbon atom. Also attached to the alpha carbon is a side chain, which is different in different amino acids (Fig. 2.2). Side chains have their properties too – some carry a positive or negative charge, some are polar and others are hydrophobic (they prefer not to be in contact with water). The different properties of the side chains are important in determining the structure and function of proteins. There are twenty different amino acids that are found in proteins. Because these can occur in different orders and combinations, this leads to a very large number of possible protein structures.
Amino acids can exist as different isomers, depending upon the arrangement of the groups attached to the alpha carbon. Isomers are defined as 'two or more different compounds with the same chemical formula but different structures and characteristics'. The alpha carbon in an amino acid participates in four covalent bonds forming a tetrahedral arrangement, and mirror image forms can exist, called enantiomers. The different enantiomers are described by the letters D and L. All amino acids occurring in proteins are L-isomers.
Amino acids are joined together by peptide bonds (Fig. 2.4). A peptide bond is formed in a reaction between the carboxylic acid group of one amino acid and the amino group of another. In the process, a molecule of water is lost and so this is called a condensation reaction.
The amino acids at each end of a protein molecule participate in only one peptide bond, hence they have either a free NH2 group or a free COOH group. The end of the polypeptide chain with a free amino group is called the N-terminus, and the end with the free carboxyl group is called the C-terminus.
2.2 Primary structure
Each protein has its own unique amino acid sequence. The sequence of amino acids in a protein defines its primary structure and this sequence is encoded by the gene for the protein.
Depending on the amino acid sequence, proteins will, under physiological conditions, preferentially adopt a particular folded structure, or conformation (see the sections on secondary and tertiary structure below). The conformation of the protein is maintained by non-covalent interactions involving amino acid side chains. These include ionic bonds between positive and negatively charged amino acid residues, hydrogen bonds, van der Waals forces and hydrophobic interactions (see Catch Up Chemistry for further information on these). Hydrophobic interactions are particularly important as they bring together non-polar amino acid side chains and ensure that these are not exposed to water. Following the initial synthesis of proteins within cells (see Chapter 5) their folding into secondary and tertiary structures is aided by the presence of other proteins called molecular chaperones.
2.3 Secondary structures
Some common patterns of folding occur. Two classical protein folds that recur in many different proteins are the alpha helix and the beta sheet (Fig. 2.5). Both of these structures depend on interactions between groups in the polypeptide backbone and they can be found in a wide range of protein molecules.
Alpha helix
This is a structure in which the polypeptide chain twists on itself in a highly regular manner. The structure is stabilised by hydrogen bonding between the C=O group of one amino acid residue and the NH group of the residue four amino acids further along the primary sequence. In this way every C=O and NH, as well as being involved in the covalent peptide bond, also participates in hydrogen bonding. This rule confers particular dimensions on the alpha helix – each turn of the helix represents 3.6 amino acid residues. Alpha helices normally assume a right-handed or clockwise twist as this is energetically more favourable. The amino acid side chains are exposed on the outside of the helix. Some amino acids, in particular proline, tend to disrupt an alpha helical structure and are known as helix breakers.
Two or more alpha helices can intertwine to form a superhelix. Such superhelices are found in proteins such as keratin, the major constituent of hair.
Beta sheet
The beta sheet, like the alpha helix, is a structure which is maintained by hydrogen bonding between C=O and NH groups, but in this case these interactions occur between adjacent strands. The amino acid side chains protrude alternately above and below the plane of the sheet. Where the adjacent strands run in a similar orientation this is said to be a parallel beta sheet; where the adjacent strands lie in opposing orientations the sheet is said to be anti-parallel. The beta-sheet structure is found in many important proteins, including antibodies.
Collagen triple helix
A third type of structure is found in collagen, an important structural protein of connective tissues. Collagen has a triple-helical structure, in which three amino acid chains are wound around each other. This structure is allowed because of the particular primary sequence of collagen and related proteins – every third amino acid residue is a glycine. Because glycine (Gly) has the smallest side chain (H) this allows the chains to interact closely to form the triple helix. Collagen-like proteins are also rich in the amino acid proline and show a repeat sequence of Gly–X–Y. Although X and Y can be any amino acid, these positions are most commonly taken by proline and hydroxyproline.
2.4 Tertiary structure
In aqueous solution, all proteins fold in such a way as to internalise those amino acid side chains that are hydrophobic and to ensure that those that are exposed to the solvent are charged or polar residues. Many alpha helices and beta-sheet structures are found to be amphipathic – this means that the hydrophobic side chains tend to occur on one side of the helix or beta sheet and the polar and charged residues on the other. In this way the protein can fold to ensure that hydrophobic surfaces interact with each other, and not with solvent.
2.5 Quaternary structure
A protein can comprise a single polypeptide chain or multiple polypeptides which are associated by covalent and/or non-covalent bonds. A common type of covalent bond is the disulphide bridge, which can occur between cysteine residues, either on the same or on different polypeptide chains. A protein which is made up of two chains is called a dimer; proteins comprising three, four and five chains are similarly called trimers, tetramers and pentamers respectively. Where a dimer consists of two identical polypeptide chains this is said to be a homodimer. Where the chains are different this is called a heterodimer. Haemoglobin, the main protein found in red blood cells, is an example of a tetrameric protein, comprising two identical alpha chains and two identical beta chains.
2.6 Domains
Proteins tend to be folded up into subunits called domains. Within a protein a single polypeptide chain can contribute one or more domains. The domains can be structurally similar or quite different from each other. Often a particular property of a protein (for example the ability to bind to another molecule or ligand) can be attributed to one domain of the protein. At the genetic level each domain is likely to be encoded by a separate exon (see Chapter 5).
2.7 Functions of proteins
Proteins carry out many functions within the body. They may form the structural elements of tissues, important for mechanical support. They can act as transporters to carry other molecules from one location to another. They can also act as hormones, which are chemical messengers that carry information from one part of the body to another. Proteins are present in cell membranes, where they may act as receptors to alert the cell to the presence of molecules in its environment. Proteins also play an important role in defence against infection.
One of the key roles of proteins is to act as enzymes. Enzymes are found in both intracellular and extracellular locations within the body and catalyse the various chemical reactions on which life depends. The table overleaf shows examples of the functions carried out by proteins.
2.8 Conformational change
In order to be fully functional, proteins must be folded correctly – they must be in their correct conformation. Protein conformation can be disrupted under a number of conditions, including extremes of pH, high temperature and in the presence of detergents. The function of proteins can also be regulated under physiological conditions by altering their conformation. Conformational change can be induced in a number of ways, for example by the binding of a ligand or by covalent modification of protein molecules. Phosphorylation is a form of covalent modification of proteins that is commonly used to regulate the activity of enzymes. The process of phosphorylation is itself mediated by enzymes called protein kinases. Another way in which protein conformation can be regulated is by cleavage. Some enzymes are synthesised as inactive precursors which only become active when they are cleaved. One such enzyme is trypsin which is found in the intestine where it plays a role in breaking down the proteins in food. The enzyme is initially synthesised in the pancreas as an inactive precursor called trypsinogen, which only becomes active when a peptide bond is cleaved. The active enzyme can then catalyse the breakdown of further trypsinogen molecules generating more active enzyme.
