You are on page 1of 50

B Human biochemistry

B1 Energy
All living things require the input of energy to exist this energy is used to drive the thousands of biochemical reactions that occur to allow the organism to grow, reproduce and sustain life. This energy comes almost always from the Sun, in the rst instance energy from sunlight is captured by photosynthetic organisms (e.g. plants, algae, certain bacteria) and converted into carbohydrates. These are then broken down by a process called cellular respiration, to produce energy-rich molecules (e.g. adenosine triphosphate, or ATP) that release energy to drive biochemical reactions. Photosynthetic organisms can by ingested by nonphotosynthetic animals, and the carbohydrates (and other biomolecules) can be broken down and used for cellular respiration. As we ourselves are non-photosynthetic organisms, we must obtain our energy through what we ingest, i.e. via our diet, so that our cells are able to carry out all the necessary biochemical reactions. The amount of energy required by an individual will depend on the amount of physical activity they perform, but in general an average man requires about 10 500 kilojoules (kJ), equating to 2500 kilocalories (kcal) per day, while an average woman needs approximately 8400 kJ (2000 kcal) per day. The amount of energy found within di erent foods we buy is often displayed on the food packaging. This energy value is worked out through a process known as food calorimetry. A food (or bomb) calorimeter can be used, which measures the heat of combustion. Here, a known mass of a particular food is ignited and completely burnt in the presence of oxygen. The energy released is transferred to water and the rise in temperature of the water is measured. The energy contained in the food can then be calculated using the following equation: q = mcT where: q = heat evolved (J) m = mass of water (g) c = speci c heat capacity of water (4.18 J g1 K1 or 4.18 J g1 C) (This is included in the IBO Chemistry Data booklet.) T = temperature change of the water (in C or K)

Learning objectives

Calculate the energy value of food using enthalpy of combustion data

1 kJ = 0.24 kcal

Worked example
When 1.00 g of tomato soup was burnt in a food calorimeter containing 100 g water, it raised the temperature of the water from 20.4 C to 28.0 C. Calculate the energy content of 100 g of tomato soup. From the equation q = mcT, for 1.00 g of tomato soup, we know that: m = 100 g c = 4.18 J g1 K1 T = 28.0 20.4 = 7.6 C (which is 7.6 K, as it is the change in temperature that we are looking at, not the actual temperature).
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011 B HUMAN BIOCHEMISTRY 1

Therefore: q = 100 4.18 7.6 = 3176.8 J, i.e. 3.18 kJ per 1 g So, in 100 g of tomato soup, there will be 3.18 100 = 318 kJ.

Examiners tip You could also be told the heat capacity of the whole system (water and calorimeter together) and asked to work out the enthalpy change. In that case, in the rst step you just multiply the heat capacity by the temperature change.

This method does not account for the heat lost through the container. The heat capacity of the thermometer and container of the food calorimeter must also be taken into account to increase accuracy of the results.

Test yourself
1 Complete combustion of 2.50 g of a snack food raised the temperature of 200.0 g of water by 17.9 C. Calculate the energy value per 100 g of the food. 2 10.0 g of a biscuit was completely combusted in a food calorimeter. The heat capacity of the whole system was 8.50 kJ C1, and the temperature of the system increased 12.1 C. Calculate the energy value of 100 g of the biscuit. 3 If 100 g of cooked rice contains 530 kJ energy, by how many degrees Celsius does the water temperature rise when 1 g of cooked rice is completely burnt in a food calorimeter containing 100 g water?

Learning objectives

Draw the general structure of a 2-amino acid and identify the di erent functional groups within the molecule Describe how amino acids behave under di erent pH values Describe how amino acids join together to form peptides Describe the primary, secondary, tertiary and quaternary structures of proteins and explain the bonding and interactions that occur between the amino acids within these structures Note the di erent types of proteins in the human body and their function Discuss the various analytical methods used to identify proteins

B2 Proteins
Structure of amino acids
Amino acids are the building blocks (monomers) of which proteins (polypeptides) are made up. There are 20 naturally occurring 2-amino acids that make up proteins in the body. These link together to form chains, and it is the sequence of these 2-amino acids in the chain that determines the overall structure (and therefore function) of the protein. These 2-amino acids have a common structure (Figure B1): they consist of a central carbon atom to which are attached four groups: 1 a carboxylic acid (COOH) 2 an amine (NH2) 3 a hydrogen (H) 4 An R group (this is di erent in each of the 20 amino acids)
H H2N C R Figure B1 General structure of a 2-amino acid. COOH

The general chemical formula of a 2-amino acid can be written as: HOOCC(R)HNH2

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

These compounds are called 2-amino acids because the amino group is on carbon 2, counting the C of the carboxylic acid group as carbon 1. For example, the amino acid shown in Figure B2 is called 2-aminoethanoic acid.

H N H
amine (amino) group

H
2

O
1

C
O H

Acidbase behaviour of 2-amino acids

Amino acids contain both acidic and basic groups in the same molecule they are thus amphoteric. Amines can accept a proton: RNH2 + H+ RNH3+ Carboxylic acids can donate a proton: RCOOH RCOO + H+ The carboxylic acid group can protonate an amino group in the same molecule. When the proton is transferred from the COOH to the NH2, a neutral ion is formed, as it bears no net charge, and this neutral form of the amino acid is known as a zwitterion (Figure B3).

carboxylic acid

Figure B2 Diagram showing the numbering on the C atoms in an amino acid.

The central carbon atom is also sometimes referred to as an -carbon, as it is next to (known as to) a carboxylic acid group. Therefore in some texts, 2-amino acids are called -amino acids.

H N H

H C R

C
O

transfer of proton

H H N+ H

H C R
zwitterion

C
O

The word zwitterion comes from the German word for hermaphrodite.

Figure B3 Formation of a zwitterion.

The pH at which this zwitterion exists is known as the isoelectric point (Figure B4) and will di er depending on the R group attached to the amino acid. This di erence in isoelectric point can be exploited analytically, as it is used to separate di erent proteins and amino acids (see Electrophoresis on page 10). When the pH of an amino acid in solution is altered, the charges on the amino acid change: The amine group is basic and therefore, at low pH, picks up a proton in acidic and neutral conditions and exists as the NH3+ group. However, as the pH is increased and the solution becomes basic, the ammonium ion loses its proton and exists in the unionised (NH2) form (Figure B4). As the pH increases, the carboxylic acid loses its proton and exists in the ionised carboxylate (COO) form.

H H3N+ C R
cation low pH

COOH

H3N+

C R
zwitterion isoelectric point

COO

H2N

C R
anion

COO

high pH

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

A bu er solution is one that resists changes in pH when small amounts of acids and alkalis are added.

Amino acids can act as buffers

We mentioned above that amino acids are amphoteric, i.e. they contain both acidic and basic groups and can therefore act as either an acid or a base.This is an important property of amino acids, as it allows them to act as bu ers. The key reason that the bu ering occurs is that the amino acids have groups that can react with H+ or OH. Any acid (H+) added is mopped up by either the COO or NH2 groups (depending on the pH) and any base (OH) added is mopped up by reaction with the COOH or NH3+ groups. It is, therefore, possible for the pH to remain fairly constant. Amino acids play an important role in bu ering the aqueous environment within cells. Signi cant changes in cellular pH can have a disastrous e ect on the biochemical reactions that take place there, as they prevent enzymes, which usually only work within narrow pH ranges, from carrying out their catalytic activity. Proteins may also change shape in low or high pH and thus lose their function.

The full explanation is a bit more complicated than this, and the various species present in equilibrium must be considered.

Examiners tip Bu er solutions are not part of the core Standard Level syllabus, but if you would like to learn a bit more about them, they are covered in the Higher Level section of Chapter 8 on page 359 of the Coursebook.

Types of amino acid

There are 20 naturally occurring 2-amino acids and therefore 20 di erent R groups. The simplest 2-amino acid is called glycine (abbreviated to Gly), where R = H. The other 19 amino acids can be grouped according to whether their R group is neutral, acidic or basic.
HL

The systematic name of glycine is 2-aminoethanoic acid, and we have seen it already in Figure B2.

Extension
All the 2-amino acids except glycine are optically active, as they possess a chiral centre. An example of an acidic amino acid is aspartic acid (Asp), which has the R group CH2COOH. An example of a basic amino acid is lysine (Lys), where R = CH2CH2CH2CH2NH2. Neutral amino acids bear neutral R groups, for example R = CH3 (alanine, Ala), R = CH2SH (cysteine, Cys) and R = CH2OH (serine, Ser).

Structure of proteins
Proteins are chains of amino acids linked together. There are estimated to be approximately a million di erent proteins in the body, and these di er only in the number and sequence of amino acids in their chains. As we shall see, the sequence of amino acids determines the overall structure (and therefore function) of the protein; it allows the protein to exist in a particular shape, this shape being maintained by bonds and forces between the di erent amino acids in the chain. The precise linear sequence of amino acids in the polypeptide chain is known as the primary structure of the protein, for example: GlyLysCysGlySerAlaAla (glycinelysinecysteineglycineserinealaninealanine) Amino acids join together to form a chain in a condensation reaction. The general reaction to form a dipeptide (two-amino acid chain) is shown in Figure B5.
4 B HUMAN BIOCHEMISTRY CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

H H2N C R H H2N C R O C N H
peptide bond

H COOH + H2N C R H C R COOH + H2O COOH

Condensation reaction: two molecules join together with the elimination of water.

Figure B5 Condensation reaction between two amino acids to form a dipeptide and water.

The amide functional group is:

O C N H

A covalent bond is formed as the carboxyl end of one amino acid reacts with the amino end of the other amino acid, and a molecule of water is lost (hence the term condensation reaction). The group that links the two amino acids is an amide, and this linkage is called a peptide bond in proteins. When two di erent 2-amino acids react together, two di erent dipeptides can be formed (Figure B6).
H H2N C H H O H N H C CH3

COOH + H2N

C CH3
alanine

COOH

H2N

COOH + H2O

CH2OH
serine

CH2OH

Ser-Ala

H H2N C CH3
alanine

H N H C

COOH + H2N

COOH

H2N

C CH3

COOH + H2O

CH2OH
serine

CH2OH

Ala-Ser

Figure B6 Formation of two possible dipeptides.

The dipeptides are di erent depending on which way around the amino acids are joined together. The rst dipeptide in Figure B6 is formed when the acid group of serine reacts with the amino group of alanine. The second dipeptide is formed when the amino group of serine reacts with the acid group of alanine. The general reaction to form a chain consisting of three amino acids (a tripeptide) is shown in Figure B7. When we write the sequence of amino acids in the chain, it is important to avoid confusion, with everyone starting from the same end of the polypeptide chain. By convention, peptide chains are always named by starting at the amino end of the chain; hence the sequence for the tripeptide in Figure B8 would be written as GlyCysSer.

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

H H2N C R

O C N H

H C R COOH + H2N

H C R COOH

H H2N C R

O C N H
peptide bond

H C R

O C N H
peptide bond

H C R COOH + H2O

Figure B7 Condensation reaction between a dipeptide and an amino acid to form a tripeptide and water.

Five other tripeptides could be formed from reacting glycine, cysteine and serine: GlySerCys, CysGlySer, CysSerGly, SerCysGly and SerGlyCys.

amino end

H C H
Gly

O C N H

H C
Cys

O C N H

H C

carboxyl end

H2N

COOH
Ser

CH2SH

CH2OH

Secondary structure of proteins

Proteins do not normally exist as linear chains they usually contain stretches in which the chain folds into regular patterns known as -helices and -pleated sheets (Figure B9). This is known as the secondary structure of a protein.

The -helix
The -helix is a helix that twists in a clockwise direction, with each complete turn consisting of 3.6 amino acids it can be likened to a corkscrew. The helical structure is stabilised (i.e. held in shape) by

H N H O C N H O C C R

O C N H O C

hydrogen bonds

H C R

R H C R O C N H O N H C C H R C H H C O H N C O N H C R H C R N H O C N H O C

R C H R C H H C O H N C O N H C R H C R

H C R

N H

C R

H C R

b -pleated sheet

Figure B9 (a) -helix; (b) -pleated sheet.

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

hydrogen bonds between the carbonyl C=O of one peptide bond and the NH of the peptide bond four amino acids below it. These hydrogen bonds are known as intramolecular hydrogen bonds, as they exist between atoms within the same peptide chain.

The -pleated sheet

-pleated

sheets consist of two or more stretches of amino acids in which the polypeptide chain is almost fully extended they take on a pleated appearance, hence the name. Intramolecular hydrogen bonds form between a C=O on one strand and an NH on an adjacent strand, which stabilises the structure.

Tertiary structure of proteins

Each polypeptide molecule has a speci c three-dimensional shape, and this is known as the tertiary structure of the protein. The tertiary structure exists because of a number of interactions between R groups (side chains) of amino acids in the polypeptide chain (Figure B10), which hold the polypeptide in a particular shape. These interactions include: hydrogen bonds between amino acids bearing side chains containing, for example, OH and N van der Waals forces between amino acids bearing hydrophobic/ non-polar side chains electrostatic forces/ionic bonds between, for example, COO and NH3+ containing side chains disul de bonds (bridges): covalent SS bonds formed by the oxidation of sulfhydryl (SH) groups within two cysteine residues. The function of the protein depends on its shape, and the shape of the protein depends on the interactions formed between the amino acids in the polypeptide chain.
Tyr

The precise sequence of amino acids is vital to the function of the protein changes in the sequence can result in loss of important interactions and therefore a change in the overall shape.

H2C
Val

CH
hydrogen bonding

O H+

H3 C H 3C

CH3 CH3 CH
Val Lys

van der Waals interactions

N HN H2C

His

Cys

CH2 S disulfide S
bridge

O
Cys

+NH3 O
ionic bonding

CH2

CH2
Asp

Figure B10 The different types of interactions that can occur between some amino acids in the peptide chain.

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

Quaternary structure of proteins

Many proteins are made up of more than one polypeptide chain. These chains are referred to as polypeptide sub-units and associate in a speci c manner this is known as the quaternary structure. The sub-units may be held together by various intermolecular interactions (i.e. interactions between groups in di erent protein chains), including hydrogen bonds, ionic interactions, van der Waals forces and disul de bonds. Proteins made up of two sub-units are known as dimers, those with three sub-units are called trimers and those with four subunits are known as tetramers. The sub-units may be identical to each other or may be di erent in structure. Examples of tetramers containing two types of sub-units are haemoglobin and immunoglobulin G, an antibody with wide immunological action in the body.

Functions of proteins
Proteins serve a variety of functions in the body. These are summarised in Table B1.

Analysis of proteins
There are various analytical techniques that can be used to identify proteins and amino acids. Here we will focus on two: paper chromatography and electrophoresis.

Paper chromatography
This is a simple method for identifying the composition of amino acids in a particular protein. The protein must rst be broken down into its constituent amino acids, and this is usually carried out by the addition of acid, such as heating
Function structural Comments provide support and strength Examples collagen (most abundant protein in body; found in tendons, cartilage, skin, bones), keratin (found in hair and nails) salivary amylase (involved in starch digestion), DNA polymerase (joins nucleotides together to form DNA), etc. (there are thousands of different enzymes in the body!) insulin (regulates blood glucose levels), growth hormone (regulates growth and cellular reproduction) antibodies (recognise and bind to foreign antigen) haemoglobin (transports oxygen), serum albumin (transports many substances, such as fatty acids, certain hormones)

biological catalysts

hormones

have a regulatory effect on specic cells/organs in the body

immunological play a key role in the ght against infection proteins transport carry materials around the body

energy source

proteins are broken down to amino acids in the body, which can enter the citric acid cycle to generate ATP (a highenergy molecule used to fuel biochemical reactions)

Table B1 Functions of proteins in the body.

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

with 6 mol dm3 HCl. The acid hydrolyses the protein by breaking the peptide bonds between the amino acids. A small sample of the resultant mixture of amino acids can then be spotted onto a piece of chromatographic paper and separated by placing the paper into a tank containing a suitable solvent (Figure B11).

tank

9.2cm

solvent front

6.7cm 3.9cm

Figure B11 Separation of amino acids using paper chromatography.

The solvent rises up the paper by capillary action and, as it does so, the amino acids travel up the paper. The extent to which each amino acid travels up the paper is dependent on how it partitions between the stationary phase (the water in the chromatographic paper) and the mobile phase (the solvent), and this is dependent on its relative solubility in each of the two phases. For example, if an amino acid is more soluble in the water (stationary) phase than the solvent (mobile) phase, it will travel less distance up the paper than if it was more soluble in the solvent phase. If the amino acid is highly soluble in the mobile phase, then it will rise higher up the paper. Once the solvent has risen to almost the top of the paper, the paper is removed from the tank. It is important to mark the distance travelled by the solvent front as soon as the paper is removed, so that the retardation factor (Rf) can be calculated. Before the Rf values can be determined, the paper must be sprayed with ninhydrin (a locating agent) this colours the amino acids purple and allows them to be visualised. Each amino acid appears as a small spot on the paper. The next step is to measure how far each spot has travelled up the paper (distance from the pencil line to the middle of the spot) and then divide this distance by the distance travelled by the solvent front (distance from original pencil line) this calculation will give you the Rf value for that particular spot: Rf = distance travelled by spot distance travelled by solvent front The Rf value is always 1 or less.

Each amino acid has a characteristic Rf value when run under the same conditions and therefore can be identi ed by comparing the Rf value of the spot with the Rf values of known amino acids.
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011 B HUMAN BIOCHEMISTRY 9

Examiners tip If your answer is greater than 1, then you know that you have gone wrong somewhere. The Rf value does not have units.

To give an example, in Figure B11, the distance to the top spot is measured and found to be 6.7 cm; the solvent front has travelled 9.2 cm from the line at which the sample was spotted. Therefore: Rf = 6.7 = 0.73 9.2

Amino acids can also be identi ed by spotting known amino acids on the paper alongside the unknown sample if a particular amino acid travels the same distance up the paper as a known one, it can be identi ed.

Electrophoresis
Another way of analysing amino acids and proteins is using a technique called electrophoresis. This technique separates charged molecules based on their ability to migrate when an electric eld is applied to the system. Both proteins and amino acids can be analysed using this technique. If the amino acid composition of a protein is to be investigated, the protein is rst treated with acid (as with paper chromatography) to hydrolyse the peptide bonds between the amino acids. The sample mixture is then applied to a support, such as paper or a polymer gel (polyacrylamide is the most common), which is saturated with a bu er of a certain pH, used as the conducting liquid. An electric eld is applied across the support, and those amino acids bearing negative charges at the bu er pH migrate to the positive electrode (anode), whereas those bearing a positive charge migrate to the negative electrode (cathode). Those amino acids with no net charge remain stationary. Detection of the amino acids is usually by staining. So what dictates the charge found on the amino acid at the bu er pH? The answer is its isoelectric point. We have already seen that the isoelectric point is the pH at which the amino acid exists in the neutral (zwitterion) form (see page 3). Remember that the di erent amino acids have di erent isoelectric points, depending on the R group attached to the central carbon. If you place an amino acid into a solution at a pH above its isoelectric point, the amino acid will carry a net negative charge and move towards the positive electrode; if the amino acid is in a solution with a pH below its isoelectric point, it will bear a net positive charge and move towards the negative electrode. Therefore, a mixture of amino acids can be separated in an electric eld at a certain pH due to the di erences in their isoelectric points. Mixtures of whole proteins can also be separated, most commonly using a polymer gel as the support medium.

Test yourself
4 2-amino acids contain both basic and acidic groups attached to the central carbon. Name the basic group and the acidic group common to all 2-amino acids. 5 Draw the tripeptide AlaGlyCys. 6 If an amino acid has an Rf value of 0.92, is it likely to be more soluble in the mobile phase or the stationary phase? 7 The isoelectric point for alanine is at pH 6.15. If alanine were placed into a bu er solution of pH 4.0 and an electric eld applied, would alanine move towards the anode or cathode?

10

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B3 Carbohydrates
Carbohydrates are widespread in nature and are, in fact, the most abundant class of biological molecules. They range from simple sugars, such as glucose and fructose, to more complex carbohydrates, such as starch and cellulose. The simplest of the carbohydrates are known as monosaccharides these can exist on their own or can join together to form polymers known as polysaccharides. Carbohydrates have a number of functions in the human body, for example: as an energy source glucose is converted into ATP to drive biochemical reactions as an energy store glucose is polymerised into glycogen and stored for times when blood glucose levels fall and energy is needed as a precursor for other biomolecules such as nucleic acids.

Learning objectives

Structure of monosaccharides
The smallest monosaccharides contain just three carbons and are known as trioses. We will, however, concentrate on those monosaccharides that contain six carbons the hexoses. Examples of hexoses are glucose and fructose; both these sugars have the same molecular formula (C6H12O6), but have di erent structural formulas. They can exist in either the straight chain form or the cyclic form (Figure B12). Glucose contains an aldehyde group and is known as an aldose, whereas fructose contains a ketone group and is known as a ketose sugar.

Describe the common structural features of monosaccharides and draw the straight-chain and ring-closed forms of glucose and fructose Describe the di erent disaccharides and polysaccharides that can be formed through condensation reactions of monosaccharides Brie y describe the main functions of carbohydrates in the human body Describe the structural di erences and similarities between starch and cellulose and explain why humans are able to digest starch but not cellulose Brie y describe what the term dietary bre means and discuss why an adequate intake is important for health and prevention of disease

The ring form of monosaccharides

In solution, the straight-chain form of the monosaccharide cyclises into a ring structure. This happens when the carbon with the double-bonded O
aldehyde O H
1

Monosaccharides have the empirical formula CH2O. They contain a carbonyl group (a ketone or aldehyde) and have at least two hydroxyl (OH) groups as part of their structure.

C C C C C OH H OH OH HO H H

CH2OH C O ketone C C C H OH OH

H HO H H

2 3 4 5

CH2OH glucose

CH2OH fructose

CH2OH O H H
1

H
4

CH2OH H H

OH

H OH
3

O OH

CH2OH OH

OH

OH H H OH Figure B12 Straight chain and ring structures of glucose and fructose.

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

11

CH2OH
5

H OH

O H OH

H OH H

H
1

OH

(carbon 1 in glucose) joins to carbon 5 via a bridging O atom. However, this can happen in two ways, so that when an OH group is formed on carbon 1 it can either be on the same side of the ring as the CH2OH group on carbon 5 (-isomer) or on the opposite side of the ring (-isomer) (Figure B13).

glucose

Disaccharides
OH
1

CH2OH
5

H OH

O H OH

H OH H

glucose

Figure B13 Structures of -glucose and -glucose. In the -isomer the OH is below the ring and on the opposite side of the ring to the CH2OH group; in the -isomer the OH is above the ring and on the same side of the ring as the CH2OH group.

When two monosaccharides join together, they form a disaccharide.This is an example of a condensation reaction, when two molecules join together with the elimination of water.This results in the formation of a glycosidic linkage between the two sugars (Figure B14).When the linkage is formed between the C1 of an -sugar molecule and the C4 of another sugar molecule, it is known as an -1,4-glycosidic linkage (or bond). Examples of common disaccharides are maltose (one of the products from the digestion of starch is made up of glucose + glucose), lactose (a major sugar found in milk, which is a disaccharide of glucose + galactose) and sucrose (common table sugar, made up of glucose + fructose).
CH2OH H OH O H OH H
1

CH2OH H OH H
4

O H OH H H

H
1

OH

OH OH glucose O

H OH glucose CH2OH H OH O H OH H H
1

CH2OH H H
4

O 1,4 glycosidic linkage H OH

H OH

H
1

H OH

+H2O

OH

maltose Figure B14 The condensation reaction between two glucose monosaccharides to produce maltose, a disaccharide.

Polysaccharides
Polymers of many monosaccharides joined together are known as polysaccharides. Examples include starch (polymer of -glucose sugars), glycogen (polymer of -glucose sugars) and cellulose (polymer of -glucose sugars). Note that all these polysaccharides are polymers of glucose. Plants convert excess glucose into starch for storage, and starch consists of a mixture of two types of glucose polymers, called -amylose and amylopectin. -amylose consists of thousands of -glucose units linked together to form linear, unbranched chains. These glucose units are linked by -1,4-glycosidic linkages (Figure B15a). Amylopectin is a branched polymer of -glucose units linked by -1,4 glycosidic linkages and -1,6glycosidic linkages at the branch points (Figure B15b). Starch is present as starch grains within plant cells, and these can be easily seen under a microscope when stained blue-black using iodine.
12 B HUMAN BIOCHEMISTRY CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

We have digestive enzymes that are able to hydrolyse the -1,4 and linkages within starch, and hence we can break down the starch polymers into smaller pieces and eventually into single glucose units, which can then be absorbed into the bloodstream and used as an energy source. Just as plants store their excess glucose in the form of starch, we store our excess glucose in the form of glycogen. Glycogen bears similarities to the structure of amylopectin, in that it is a branched polymer of -glucose units linked by -1,4-glycosidic linkages and -1,6-glycosidic linkages. It is more highly branched than amylopectin and is stored as granules within cells in particular, liver and skeletal muscle cells. Glycogen is digested back into glucose when energy is needed. Cellulose, found in plant cell walls, is a polysaccharide responsible for giving structure and strength to plants examples include wood and cotton. It, too, is made up of glucose units, but in this case, the glucose units are in the form of -glucose, i.e. the OH is on the same side of the ring as the CH2OH. This means that the glycosidic linkages between the glucose units are also and are known as -1,4-glycosidic linkages (Figure B16). The glucose units in cellulose are linked by -1,4-glycosidic linkages; we do not possess the enzyme (known as cellulase) that hydrolyses these linkages, and therefore we (and most other animals) cannot digest cellulose.
-1,6

Certain plants have a high starch content within their cells: for example, potato tubers, rice grains and wheat. These are the major sources of carbohydrate in the human diet.

Note that cellulose is made up of linear chains and is not branched. The polymer chains lie side by side and form many hydrogen bonds between glucose units within the chains and between the chains, giving the cellulose structure its strength.

CH2OH

CH2OH

CH2OH

CH2OH

O H OH H H OH

H O

O H OH H H OH

H O

O H OH H H OH

H O

O H OH H H OH

a amylose

CH2OH

CH2OH

O H OH H H OH

H O

O H OH H H

H

O OH
CH2

CH2OH

CH2OH

CH2OH

O H OH H H OH

H O

O H OH H H OH

H O

O H OH H H OH

H O

O H OH H H OH

b amylopectin

Figure B15 Examples of how the glucose units are joined in (a) amylose and (b) amylopectin.

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

13

CH2OH

O H OH H H OH

OH

CH2OH

OH

OH H
CH2OH

H O

H O

O H OH H H OH

O H H

OH H
CH2OH

H O

cellulose

Figure B16 Glucose units joined together in cellulose.

Herbivores such as cows survive on a diet of cellulose-rich plants such as grass. These animals have an extensive digestive system that contains bacteria that secrete cellulase, and this allows the breakdown of cellulose into smaller units for digestion.

Dietary bre
Dietary bre is plant material that we ingest but are not able to digest. It passes through the gut relatively intact, as we do not possess cellulase enzymes capable of hydrolysing it. There are two types of dietary bre. 1 Insoluble bre: this includes cellulose, hemicellulose and lignin found in plant cell walls. As it passes through the gut, it binds water and softens and adds bulk to the faeces. Dietary sources include whole grains (such as wheat), vegetables and beans. 2 Soluble bre: this includes pectin found in plant cells; sources include oats, oatbran and beans. Dietary bre has been linked to having a bene cial e ect on a number of conditions/diseases: a high- bre diet is useful in treating and preventing constipation, haemorrhoids and diverticulosis (formation of small pouches in the colon) and may improve some cases of irritable bowel syndrome (IBS) Crohns disease is a condition caused by in ammation of the bowel wall; a diet high in bre is one form of treatment for this condition a high- bre diet may help in overcoming obesity, as bre provides bulk to a meal yet contains relatively few calories, as it is not digested soluble bre has been shown to reduce cholesterol levels by lowering LDL (see page 21); therefore, a diet rich in soluble bre has been linked to having a bene cial e ect on reducing the incidence of heart disease bre, especially soluble bre, has been shown to slow the absorption of glucose and thus lead to a lowering of blood glucose levels; it may thus lower the risk of developing diabetes mellitus.

Test yourself
8 Is the following sugar an -sugar or a -sugar?
CH2OH H OH O H OH H H OH OH H OH H

9 A disaccharide is shown below. State the type of reaction that resulted in its formation and name the linkage between the two rings.
CH2OH O H OH H H OH H O H CH2OH O H OH H H OH OH H

14

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B4 Lipids
The word lipid comes from lipos, the Greek word for fat. There are various types of lipid in the human body: for example, steroids (e.g. cholesterol, a steroid that is abundant in cell membranes and also is a precursor for many steroid hormones), triglycerides (found in fatty (adipose) tissue and act as an energy store) and phospholipids (found in cell membranes). These three lipids have something in common they are all hydrophobic in nature and thus are not soluble in water; they are, however, soluble in non-polar or weakly polar organic solvents such as trichloromethane (CHCl3) and ethoxyethane (CH3CH2OCH2CH3). Lipids are hydrophobic molecules that contain carbon, hydrogen and oxygen in various proportions (the predominant atoms are carbon and hydrogen, and therefore the chains are nonpolar); some types of lipid can also contain other atoms such as phosphorus and nitrogen (in phospholipids).

Learning objectives

Triglycerides
Tricglycerides are the most abundant class of lipids and make up the majority of lipids in the diet; fats and oils consist of triglycerides. Fat (as triglycerides) is found in cells known as adipocytes, which make up adipose (fatty) tissue. Adipose tissue has a number of roles in the body: it acts as a major energy reserve; it provides insulation from heat loss through the skin; and it insulates, protects and supports organs such as the heart and kidneys. Fat is an important energy store in the body, as it has a higher energy value than carbohydrate or protein. In other words, more energy is released per gram of fat than per gram of carbohydrate or protein. Energy is obtained from food in a process called cellular respiration. This is where food molecules, such as fat (as fatty acids) and carbohydrates (as glucose) are oxidised by a series of enzyme-catalysed reactions to ultimately produce carbon dioxide and water. The carbon atoms in fatty acids are less oxidised than in carbohydrates or protein, and thus they are able to undergo more oxidation, resulting in the release of more energy. Triglycerides are non-polar, hydrophobic molecules. They are formed by condensation of three fatty acids with the three alcohol groups of glycerol (propane-1,2,3-triol) (Figure B17). The functional group formed is an ester group, and so this reaction can also be called esteri cation. Fats yield approximately 37 kJ energy per gram, whereas carbohydrates and protein yield approximately 16 kJ per gram each.

Compare the structures of triglycerides, steroids and phospholipids Describe the condensation of glycerol and free fatty acids to a triglyceride Explain why fats are higher in energy than carbohydrates De ne the term iodine number and use addition reactions to calculate the number of carbon carbon double bonds in an unsaturated fat/oil Describe the structural di erences between saturated and unsaturated fatty acids and explain how the composition of fats is related to their melting point Describe the structures of the omega-3 and omega-6 essential fatty acids and discuss their importance to health Explain the di erences between the structures and function of HDL- and LDL-cholesterol and outline their role in the development or prevention of disease Describe the digestion of triglycerides Discuss the roles of lipids in the body and their impact on health and disease

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

15

removal of water

O C O R

CH2 CH

HO

HO

C O

CH2

HO

Triglycerides are not usually made up of the same fatty acid they usually contain di erent fatty acids.

glycerol

fatty acids

O CH2 O C O CH O C O CH2 O C

Examiners tip The esteri cation reaction is not on the Standard Level syllabus. See the Higher Level section of Chapter 10 on page 471 of the Coursebook for further details of esteri cation.

+ 3H2O

triglyceride

Figure B17 Condensation of glycerol with three fatty acids to form a triglyceride, where R, R and R are long-chain hydrocarbons. Each individual reaction is a condensation reaction and results in the elimination of water.

Fatty acids contain a long hydrocarbon chain with a carboxylic acid (COOH) at one end. They have the general formula: CH3(CH2)nCOOH.

Fatty acids
Fatty acids usually contain between 14 and 22 carbon atoms, but fatty acids with 16 and 18 carbon atoms are the most common (note that they contain an even number of carbon atoms). There are two major types of fatty acids: 1 those that have only carboncarbon single bonds (saturated fatty acids) 2 those that contain one or more carboncarbon double bonds (unsaturated fatty acids). Monounsaturated fatty acids contain only one C=C, whereas polyunsaturated fatty acids contain two or more C=C. The C=C in fatty acids is almost always cis, and this results in a bend (or kink) in the hydrocarbon chain (Figure B18).

cis and trans (geometrical) isomerism is not covered on the Standard Level core syllabus. See the Higher Level part of Chapter 10 on page 487 of the Coursebook for more detail on this.

Iodine number
It is possible to work out the degree of unsaturation, i.e. the number of double bonds, within a fat or oil, using iodine. Iodine is able to add across a double bond, as shown in Figure B19. As you can see, one molecule of iodine reacts with one C=C, so the number of moles of iodine used up in the reaction with a fat or oil can be equated to the number of double bonds within the fat or oil molecule. For example, if two moles of iodine reacted with one mole of fat or oil, then that would indicate that there were two C=C within the fat or oil molecule.

16

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

HO C O

CH2 CH2

CH2 CH2

CH2 CH2

CH2 CH2

CH2 CH2

CH2 CH2

CH2 CH2

CH2 CH2

CH3

CH3(CH2)16COOH
stearic acid: saturated fatty acid

CH2 CH2 CH2 CH2 CH2 CH2 CH2

CH3

CH3 CH2

HC CH CH2 CH CH2 CH

HO C O

CH2 CH2

CH2 CH2

CH2 CH2

CH2 HC

CH

CH3(CH2)7CH=CH(CH2)7COOH
oleic acid: monounsaturated fatty acid

HO C O

CH2 CH2

CH2 CH2

CH2 CH2

CH2 HC

CH

CH3(CH2CH=CH)3(CH2)7COOH
linolenic acid: polyunsaturated fatty acid

Figure B18 Examples of saturated and unsaturated fatty acids. All double bonds shown have cis geometry (see Chapter 10, page 489 in the Coursebook). I C C + I2 C I C

unsaturated fat

Figure B19 The addition reaction between iodine and the double bond in an unsaturated fatty acid.

A measure of the degree of unsaturation in a fat or oil may be given by the iodine number. A saturated fat with wholly saturated fatty acids will have an iodine number of zero, whereas an oil consisting of mostly polyunsaturated fatty acids will have a high iodine number. For example, if 65 g of iodine reacted with 50 g of fat or oil, then the iodine number would be: 65 2 = 130 (as the iodine number refers to the number of grams of iodine that reacts with 100 g of fat/oil). An iodine number of 130 would suggest that the oil contains a high degree of polyunsaturated fatty acids such as linolenic acid (which has three C=C). An animal fat, such as butter, which has a high degree of saturated fatty acids, has an iodine number of between 25 and 45.

The iodine number is the number of grams of iodine that reacts with 100g of fat or oil.

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

17

Worked example
Work out the iodine number, given the structural formula of linoleic acid: CH3(CH2)4(CH=CHCH2)2(CH2)6COOH Mr = 280.4 (Mr for I2 = 253.8)

To work out the iodine number of a known fatty acid, we must look at the number of double bonds in the fatty acid. Linoleic acid has two double bonds, and thus two moles of iodine (I2) will react with one mole of linoleic acid. This means that 280.4 g of linoleic acid would react with 253.8 2, i.e. 507.6 g I2. 100 g of linoleic acid would therefore react with: 100 507.6 = 181 g I2 280.4 Thus the iodine number for linoleic acid is 181.

Most triglycerides contain a mixture of saturated, monounsaturated and polyunsaturated fatty acids: those fats that are predominantly made up of saturated fatty acids are known as saturated fats; those containing predominantly monounsaturated fatty acids are called monounsaturated fats (oils); and those with predominantly polyunsaturated fatty acids are polyunsaturated fats (oils).

Fats and oils

The level of unsaturation in the fatty acids in uences the melting point of the fat or oil: triglycerides with a high proportion of saturated fatty acids have higher melting points and are solid at room temperature, e.g. animal fats such as lard and butter. This is due to the long hydrocarbon chains being able to pack closely together, forming intermolecular interactions (van der Waals forces). Triglycerides rich in monounsaturated and polyunsaturated fatty acids, on the other hand, have lower melting points and are oils at room temperature (e.g. vegetable and sh oils). As we have already seen, the C=C results in the formation of a bend within the hydrocarbon chain. As a result, the hydrocarbon chains are not able to approach each other as closely and form as many intermolecular interactions, hence the lower melting point. As the number of C=C increases within the triglycerides, they become more and more uid, hence polyunsaturaterich triglycerides have lower melting points than monounsaturate-rich ones, although both types are liquids at room temperature. It is customary to call solid triglycerides fats and liquid triglycerides oils.

Omega-3 and omega-6 fatty acids

We obtain the majority of fatty acids that we need via our diet, although we are able to synthesise most in the body. Two fatty acids which must be obtained from the diet, as we do not possess the necessary enzymes to biosynthesise them, however, are linoleic acid and linolenic acid these are known as essential fatty acids, and dietary sources include linseed oil, rapeseed oil and soybeans. Linolenic acid is also known as an omega-3 fatty acid, and linoleic acid as an omega-6 fatty acid. The omega refers to the position of the rst C=C, when the fatty acid is numbered starting with the carbon at the opposite end to the carboxyl carbon (COOH group) (Figure B20). For example, linoleic acid has two C=C positioned at the sixth and ninth carbons from the terminal CH3, but it is the rst C=C that is used to categorise it as an omega-6 fatty acid. Linolenic acid has three
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

We would normally name a carboxylic acid containing C=C counting the C of the COOH group as carbon 1. Omega is the last letter of the Greek alphabet and indicates that we are starting from the end of the chain.

18

B HUMAN BIOCHEMISTRY

O C HO
linoleic acid

6
omega-6 fatty acid

4 5 3

2 1

O C HO
linolenic acid

6
omega-3 fatty acid

4 5

3 2

Figure B20 Linoleic acid and linolenic acid, drawn without the bends in the structures for clarity.

C=C: one C=C at the third carbon starting at the opposite end to the carboxylic acid, the second at the sixth carbon, and the third at the ninth carbon. It is thus an omega-3 fatty acid, as the rst C=C is at carbon 3. A diet rich in omega-3 fatty acids has been shown to have several bene ts on health. A regular intake of eicosapentaenoic acid (EPA) (a longer-chain derivative of linolenic acid found in oily sh such as salmon) and linolenic acid (found in ax seeds, soybeans and rapeseed oil) can reduce the risk of heart attacks by lowering LDL-cholesterol (see below) and triglyceride levels in the bloodstream. Omega-3 essential fatty acids have also been associated with brain function and are sometimes included in dietary supplements for pregnant women, to help boost brain development in the growing fetus.

Trans fats
We have already seen that fats and oils can undergo addition reactions across the C=C with iodine. Addition reactions may also be used in the food industry, except this time using hydrogen to add across the C=C double bonds in the unsaturated fatty acid, thus converting C=C double bonds to CC single bonds. This results in what are called hydrogenated fats, which have higher melting points, due to a higher degree of saturation, and are therefore more solid at room temperature. Hydrogenated fats were used in margarines and also in many processed foods, as they prolong shelf-life (see Option F on the CD-ROM, page 7). However, there is now a move to use alternatives to hydrogenated fats, as they have been shown to have a negative e ect on health. This is due to the formation of trans fats during the hydrogenation process, in which trans double bonds are formed in the fatty acid chain. Trans fats are associated with an increase in the levels of LDL-cholesterol (see later) and thus an increase in the risk of heart disease.

Digestion of fats
When fats are ingested, they must be broken down into smaller molecules in order to be absorbed into the body from the intestines. This breakdown is catalysed by enzymes (e.g. pancreatic lipase), which are secreted into the intestines. These enzymes catalyse the hydrolysis of the ester bonds in the triglycerides into free fatty acids plus glycerol (propane-1,2,3-triol), which are then absorbed (this is the reverse of the formation reaction shown in Figure B17). Once absorbed, the fatty acids and glycerol are reassembled into the triglycerides and transported to their destination.
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011 B HUMAN BIOCHEMISTRY 19

Because they are hydrophobic (non-polar) molecules, they are poorly soluble in the aqueous blood plasma and cannot be transported as free molecules. Therefore they are transported via carriers called lipoproteins. Lipoproteins play an important role in heart disease, and we shall talk more about them when we look at the transport of lipids.

Phospholipids
The second major type of lipid in the body is the phospholipids.These are the main lipids found in cell membranes. A membrane made up of a bilayer of phospholipids surrounds each cell, and phospholipid membranes also surround many of the inner structures (called organelles) within the cells. Phospholipids are similar in structure to triglycerides, in that they contain two fatty acid chains esteri ed (ester linkage) to two of the alcohols of glycerol. However, they also contain a phosphate group, which has reacted with the third alcohol of glycerol (phosphate ester linkage). The phosphate also usually undergoes a condensation reaction with an amino alcohol, for example, choline (Figure B21) to form a second phosphateester linkage. A phospholipid bearing a choline alcohol is called phosphatidyl choline (also known as lecithin). Phospholipids therefore have a polar head (the phosphate ester) and a non-polar tail (the two fatty acids). This property allows them to form bilayers when placed in an aqueous environment, as they arrange themselves so that
CH3 H3C
choline

N+ CH2 CH2 O

CH3

phosphate

P O

O

glycerol

H2C O C

HC O OC

CH2 O

fatty acids

phospholipid bilayer phosphatidyl choline

Figure B21 Structure of phosphatidyl choline and a representation of the lipid bilayer.

20

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

the polar head groups are in contact with the water (to form hydrogen bonds) while the non-polar tails minimise their exposure to the water and interact with each other in the interior of the bilayer (Figure B21).

Steroids
The third main type of lipids in the body is the steroids. Examples include cholesterol, the sex steroids (testosterone and oestrogen) and adrenal hormones (hydrocortisone and aldosterone). Steroids are hydrophobic (mostly non-polar) molecules, bearing a common structure, known as the steroid backbone. This is made up of three six-membered rings (called A, B and C) and a ve-membered ring (called D) fused together. The steroids vary depending on the type and position of substituents on the steroid backbone. There is also usually a carboncarbon double bond in either ring A or ring B. Oestrogens are di erent to the other steroids, in that they have an aromatic A ring (benzene ring). Cholesterol (Figure B22) is a major steroid found in the body. It is found in cell membranes, where it maintains uidity of the membrane, and it is also the precursor of other steroids, such as those mentioned above, as well as bile acids and vitamin D. Although cholesterol plays an important role in the body, it can also have a negative e ect on health, in that it can contribute to heart disease.
H3C CH3 CH CH3 CH2 CH2 CH2 CH H3C A HO
cholesterol

CH3 C B
steroid backbone

Figure B22 Structure of cholesterol and the steroid backbone.

Transport of lipids
Triglycerides and cholesterol are essentially insoluble in the aqueous blood plasma and therefore cannot be transported as free molecules. Therefore, these lipids assemble with phospholipids and proteins to form particles known as lipoproteins. The inside of the lipoprotein is hydrophobic, but the outside is hydrophilic and therefore can travel in the bloodstream. There are di erent types of lipoprotein, classi ed according to their relative densities. Each type has a di erent composition of protein, triglycerides and cholesterol. Low-density lipoproteins (LDL) consist mainly of cholesterol and are the major reservoir of cholesterol they transport it throughout the body, where it can be stored in the tissues or used (for example, in cell membranes). High levels of this LDLcholesterol can lead to fatty deposits in the walls of arteries in the heart and elsewhere, leading to atherosclerosis (hardening of the arteries), which can result in heart attack and stroke. Another lipoprotein is high-density lipoprotein (HDL) this is a protein-rich particle. It is smaller than LDL and denser, as it contains more protein (protein is more dense than lipid). HDL consists of approximately 33% protein, compared with 25% protein for LDL. HDL scavenges
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011 B HUMAN BIOCHEMISTRY 21

Low LDL-cholesterol levels and high HDL-cholesterol levels reduce the risk of heart disease.

cholesterol from LDL, tissues and artery walls and returns it to the liver, where it is converted to bile acids. Thus, HDL removes cholesterol from the tissues and arteries and has a bene cial e ect with regards to heart disease. LDL-cholesterol levels are not based on the amount of cholesterol taken in the diet but rather on the amount and type of fat taken in. Saturated fats (especially myristic, palmitic and lauric acids) and trans fats increase the level of LDL-cholesterol in the body and are thus associated with an increased risk of heart disease. Trans fats have also been found to lower HDL-cholesterol levels. Polyunsaturated and monounsaturated fats, however, have been shown by some studies to lower LDL-cholesterol and increase HDL-cholesterol. Therefore, the majority of fat taken in the diet should be in the form of mono- and polyunsaturated fats, while intake of saturated fats and trans fats should be limited (or totally excluded) in order to reduce LDLcholesterol levels. Table B2 summarises the roles of the various lipids and gives some of their positive or negative e ects.
Type of lipid triglycerides Effects / roles energy reserve insulates and protects organs insulates from heat loss through the skin monounsaturated, polyunsaturated fatty acids and omega-3 fatty acids protect against heart disease by lowering LDLcholesterol saturated fats such as lauric, myristic and palmitic acids increase risk of heart disease by increasing LDL-cholesterol high fat intake associated with obesity major component of cell membranes cholesterol helps to maintain the uidity of cell membranes and is a precursor for sex steroids, adrenal hormones, bile acids and vitamin D high LDL-cholesterol levels are associated with atherosclerosis and heart disease

phospholipids steroids

Table B2 Functions and effects of the major groups of lipids.

Test yourself
10 Is the following fatty acid saturated or unsaturated? Would you expect a fat consisting mainly of this type of fatty acid to be liquid or solid at room temperature?
O C HO

11 Is the following fatty acid an omega-3 or omega-6 fatty acid?

O C HO

12 The formulas of some fatty acids are shown below. Deduce the number of C=C in each and hence work out the iodine number (Mr for I2 = 253.8). C15H23COOH C17H33COOH C19H35COOH C13H27COOH 13 A fatty acid with Mr = 254.46 has an iodine number of 100. Work out the number of C=C in the fatty acid.

22

B HUMAN BIOCHEMISTRY

B5 Micronutrients and macronutrients

Nutrients are chemical substances derived from food that are used by the body for growth and survival. We have so far discussed proteins, carbohydrates and fats. All these are required in relatively large amounts in the diet they are known as macronutrients, and other examples include minerals such as sodium, magnesium, potassium, calcium, phosphorus, sulfur and chlorine. Macronutrients are chemical substances that are required in relatively large amounts (>0.005% body weight) by the body. Micronutrients, by contrast, are required in very small amounts by the body (<0.005% body weight). Examples include vitamins and trace minerals such as iron, copper, zinc, iodine, selenium, cobalt and manganese. Their main functions are as co-factors for enzymes (a co-factor is a non-protein component of an enzyme that is essential for its correct functioning), but they may also be incorporated into certain hormones. They are required in mg or g amounts, and some, if taken in high amounts, can be toxic, e.g. the trace minerals. Iodine is an important component of thyroid hormones.

Learning objectives

Explain the di erence between micro- and macronutrients and give examples. Compare the structures of vitamins A, C and D and relate their structures to their relative solubilities in water or fat Deduce whether a vitamin is water- or fat-soluble by looking at its structure Discuss the di erent types of nutrient de ciencies around the world, and the diseases they lead to, and suggest ways of solving the de ciency problems

Vitamins are micronutrients

Vitamins are organic molecules that are essential in small amounts for the normal functioning of the body. There are two main classes of vitamins: water-soluble vitamins and fat-soluble vitamins. Water-soluble vitamins have structures that contain polar groups, for example OH groups, which can hydrogen bond to water molecules. Examples include vitamin C (also known as ascorbic acid) and the B group of vitamins (a group consisting of eight di erent vitamins); these are readily excreted in the urine and stores are rapidly depleted, so a regular daily intake is required. Fat-soluble vitamins are mostly hydrophobic (non-polar) in nature, consisting of long hydrocarbon chains or rings. Examples include vitamins A, D, E and K. This type of vitamin is stored in the body, and therefore, if excessive amounts are taken, levels can build up, resulting in toxicity.

Vitamin C (ascorbic acid)

This is a water-soluble vitamin, as it contains a number of hydroxyl groups, which enable it to form hydrogen bonds with water (Figure B23).Vitamin C plays a key role in tissue growth and repair more speci cally, it is required for the synthesis of collagen, a protein found in connective tissue (for example, in bone, skin and blood vessels). It can also act as an antioxidant, protecting the body from damage by free radicals produced naturally during normal metabolic processes.Vitamin C is found widely in fresh fruit and vegetables, particularly in citrus fruits. De ciency of vitamin C results in the disease called scurvy, symptoms of which include swollen, bleeding gums, muscle and joint pain, and poor healing of wounds.
H H HO C C H HO OH OH H O O

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

23

Vitamin A (retinol)
Vitamin A (Figure B24a) is a fat-soluble vitamin. It contains a long hydrocarbon chain and a hydrocarbon ring, and although it does contain a hydroxyl group, the polar nature of this group is not enough to o set the non-polar nature of the rest of the molecule. Having mostly a non-polar structure means that it is soluble in fat rather than water. Vitamin A is important for vision, especially in low-light intensities; it also plays a role in growth and development, skin repair and the immune system.Vitamin A (in the form of retinol) is found in animal products, such as liver, egg yolks and dairy products. It can also be formed in the body from beta-carotene, a vitamin A precursor, found widely in fruit and vegetables such as carrots. De ciency of vitamin A results in a condition known as xerophthalmia, a severe drying of the eye, accompanied by night blindness; it is a leading cause of blindness in children in developing countries. Examiners tip You should be able to work out from its structure whether a particular vitamin is wateror fat-soluble.Vitamins containing many OH groups and/or several very electronegative atoms (such as N or O) are generally watersoluble, and those that consist almost entirely of C and H are fat-soluble.

Vitamin D (cholecalciferol)
Vitamin D is a steroid derivative; it is not a steroid, because it does not have the characteristic steroid backbone (Figure B24b). It contains one polar hydroxyl group and a large non-polar hydrocarbon backbone, making it predominantly hydrophobic and therefore fat-soluble.Vitamin D plays an important role in promoting the absorption of calcium and phosphorus from food and in promoting mineralisation of bone; it is present in butter, cheese, milk and sh liver oil.Vitamin D can be synthesised in the body by the action of sunlight on pro-vitamins in the skin, but de ciency can occur, for example in those with limited exposure to sunlight, and also in children, who require larger levels of vitamin D for growth.Vitamin D de ciency in children can lead to a condition called rickets, characterised by softening and deformity of the bones.
b

H3C

CH3

CH3 H C C CH C H H C C H

CH3 CH2OH C H

CH2 H2C CH2 HC CH3 CH3

CH3

vitamin A (retinol)

HO

vitamin D (cholecalciferol)

Figure B24 Structures of the fat-soluble vitamins: (a) vitamin A; and (b) vitamin D.

Malnutrition
Malnutrition is the term used to describe an inadequate intake of the nutrients needed to maintain good health. It can be caused by not eating enough food and also from eating a poorly balanced diet: for example, a diet of processed, fast foods, which lack necessary vitamins and minerals. The problem of insu cient food intake is not just a problem in the poorer developing countries: certain groups of the population in industrialised countries are also at risk, for example, the elderly. Poorly balanced diets are a growing problem in countries such as the USA and the UK, where obesity levels are rising and diets rich in over-processed, high-fat, low-nutrient foods, are increasingly common.
24 B HUMAN BIOCHEMISTRY CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

Micronutrient deciencies

Iron is a component of haemoglobin and is required for O2 transport. A lack of iron in the diet leads to a reduced amount of haemoglobin and red blood cells in the body, known as anaemia, symptoms of which include feeling tired, breathlessness and palpitations. Iron de ciency is thought to be the commonest micronutrient de ciency in the world and occurs not just in developing countries but also industrialised countries. Iron-supplementation of foods, such as breakfast cereals, is one strategy to overcome this problem and has proved to be successful in a number of countries. Iodine in the diet is used to synthesise the thyroid hormone thyroxine, which plays a major role in controlling the basal metabolic rate in adults and growth and development in children. De ciency of iodine results in a condition called goitre (or goiter), characterised by a lump around the throat area caused by an enlarged thyroid gland. Addition of iodine to table salt has resulted in a substantial decrease in iodine de ciency. Vitamin A de ciency can result in a condition called xerophthalmia, which, as we have already mentioned, is a leading cause of blindness in many developing countries. Forti cation of foods with vitamin A has proved a successful strategy at combating this de ciency. Forti cation of margarine has produced great success in many countries, but other foods are also showing promise for example, sugar forti cation (used in Central America) and maize forti cation (in Zimbabwe). Vitamin B group: vitamin B3 (called niacin) is converted to a coenzyme that plays a key role in oxidationreduction processes in the cell. De ciency results in a condition called pellagra, characterised by diarrhoea, dermatitis and dementia.Vitamin B1 (thiamine) is converted to a coenzyme that is necessary for energy production within the cell. De ciency leads to beriberi, characterised by muscle weakness. Many foods, such as breakfast cereals, are forti ed with niacin and thiamine, and de ciency is rare in developed countries. Vitamin C de ciency results in scurvy. Scurvy used to be a common problem among sailors, who spent long periods at sea without fresh fruit and vegetables, before it was recognised that a regular intake of citrus and other fruits and vegetables would prevent this disease. Nowadays, scurvy is rare in developed countries. Vitamin D de ciency can result in rickets in children. As explained above, it is a condition in which softening and deformity of the bones occur due to a reduction in uptake of calcium and phosphate from food. Forti cation of dairy products with vitamin D means that de ciency is now rare in industrialised countries. However, it is still a problem in some developing countries, where intake of dairy products may be low, or where religious or social customs and/or climatic conditions prevent an adequate exposure to sunlight. Selenium is important for the functioning of certain enzymes, which mop up peroxides in the cell. Selenium is found in the soil and is taken up by plants such as cereal crops; the milling process of the grain does not remove the selenium, and thus it is usually taken in the diet in su cient quantity to prevent de ciency. However, in certain areas of some countries, such as Russia and China, selenium levels in the soil are too low, and in these cases selenium supplements are required.
B HUMAN BIOCHEMISTRY 25

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

Macronutrient deciencies
Protein Protein de ciency is one of the most common forms of malnutrition in developing countries and is associated with millions of deaths per year; it is most common in young children at the time of weaning. There are two types: marasmus and kwashiorkor. Marasmus is malnutrition caused by an inadequate intake of both protein and energy, and is characterised by a thin, emaciated appearance and stunted physical and mental development if the condition persists. Kwashiorkor is malnutrition caused by an inadequate intake of protein but an adequate energy intake; children with this condition usually have a large belly, with stunted growth. These conditions have a high death rate because they also result in a weakening of the immune system, so that it is more di cult to ght infections; a large number of children with protein de ciency in developing countries die from infections rather than from the starvation itself.

Causes of deciencies
The types of nutritional de ciencies we have seen above are caused by: food shortages in developing countries, due to lack of modern agricultural methods, such as fertilisers and irrigation poor food distribution and high food prices chronic (long-term) illness, such as chronic infections, resulting in decreased appetite, reduced ability to absorb nutrients, and excessive excretion of nutrients due to chronic diarrhoea poor diet due to lack of education or understanding of what constitutes a balanced diet.

Some solutions

provision of energy- and nutrient-rich food rations forti cation of staple foods with micronutrients genetic modi cation of food: for example, growing rice containing beta-carotene to prevent vitamin A de ciency-related blindness in children in developing countries provision of nutritional supplements help with implementation of modern agricultural methods in developing countries improving education with regards to how to eat a balanced diet.

Test yourself
14 Would you expect the following vitamin to be fat- or water-soluble?
O

26

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B6 Hormones
Hormones are chemicals messengers they allow cells in the body to communicate. They cause a speci c e ect on hormone-sensitive cells (called target cells) in the body and the e ect they cause depends on the type of hormone and also the type of target cell. Hormones are produced in glands known as endocrine glands (the study of the hormone system is called endocrinology). The endocrine glands secrete the hormones directly into the blood, where they then a ect cells from other organs, or from the organ from which they were released. When the hormone reaches the target cell, it binds to a speci c protein, known as a receptor, either on the surface of the cell or inside the cell. It is the binding of the hormone to the receptor that triggers the target cell to produce a response. There are many di erent types of hormone in the body; some are proteins (e.g. insulin, antidiuretic hormone (ADH)), some are steroids (e.g. oestrogen, testosterone, progesterone, aldosterone) and some are amino acid derivatives (e.g. thyroxine, epinephrine).

Learning objectives

Describe how and where hormones are produced and explain their roles in the body Describe the structural di erences and similarities of cholesterol and the sex hormones Outline how combined oral contraceptives work to prevent pregnancy Describe the medical and nonmedical uses of steroids

Proteins and peptides as hormones

Insulin
The endocrine gland that produces insulin is the pancreas. Insulin is a protein secreted into the bloodstream in response to high levels of glucose in the blood. Insulin binds to insulin receptors on target cells to decrease the amount of blood glucose by: increasing the uptake of glucose in these cells (for example, muscle cells and most other tissue cells) and increasing utilisation of glucose within these cells, to produce energy stimulating the liver to store glucose in the form of glycogen. A common metabolic disease, known as diabetes mellitus, is caused by either a de ciency of insulin or a reduction in the response of target cells to insulin (known as insulin resistance). The e ect is high levels of glucose in the blood, which can lead to long-term complications such as nerve damage, kidney failure, heart disease and stroke.

ADH is a short peptide produced in the pituitary gland in response to an increase in osmotic pressure in the blood and also a reduction in plasma volume (signs of dehydration). The main target cells of ADH are the kidney tubules, which are made more permeable; there is an increase in the uptake of water, resulting in more water being retained in the body and less lost in the urine.

Steroid hormones
The steroid hormones include the corticosteroids and the sex steroids.
Aldosterone Aldosterone is produced in the adrenal glands, in the adrenal cortex. It is known as a corticosteroid and regulates the salt and water balance in the body. It acts on the kidney tubules to increase the uptake of sodium and water and to promote the loss of potassium.
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011 B HUMAN BIOCHEMISTRY 27

Oestrogen and progesterone Oestradiol is the most potent oestrogen (others are oestrone and oestriol). It is produced in the ovaries in pre-menopausal women and has e ects on many types of cell in the body, for example, breast cells and endometrial cells (lining the uterus). It is responsible for promoting female secondary sexual characteristics, such as breast development, and also for regulating the menstrual cycle (along with progesterone) and maintaining pregnancy. Progesterone is also produced in the ovaries and prepares the body for conception by preparing the endometrium for implantation of an egg. If pregnancy occurs, it helps maintain pregnancy (during pregnancy, it is produced in the placenta) and prepares the body for birth. Testosterone Testosterone is a male sex hormone (known as an androgen) produced in the testes and has e ects on many cells in the body. It is responsible for promoting the male secondary sexual characteristics, such as deepening of the voice, increase in muscle mass and strength, facial hair, etc.

Amino acid derivatives as hormones

Thyroxine
Thyroxine is an amino acid derivative containing iodine. It is produced in the thyroid gland and has e ects on all cells. It regulates metabolism, controlling the amount of oxygen used up by cells. It is responsible for generating body heat and for growth and development. Hypothyroidism (in which the thyroid gland does not produce enough thyroxine) is a common disorder, increasing with age, and results in a slowing of metabolism, characterised by weight gain, tiredness and feeling cold.

Epinephrine is secreted by the adrenal glands (in the medulla) and is a major hormone of the part of the nervous system that prepares the body for stressful situations. It acts on many cells of the body, for example, the brain, muscles, blood vessels, heart, lungs and digestive system. It has many e ects, including: increasing blood pressure, and the strength and rate of heart contractions, to pump more blood to the muscles; increasing the breakdown of glycogen in the liver, to raise blood glucose levels so that they can be utilised by cells; and dilating the vessels in the lungs so that more oxygen can be supplied to the heart and muscles. All these e ects allow the body to deal with emergency situations, called the ght or ight response.

Structure of steroid hormones

Steroid hormones all have a common structure, in that they all contain a steroid backbone consisting of three six-membered rings and a vemembered ring fused together. This was already touched on when we talked about cholesterol. If we take cholesterol and the sex steroids as examples, we can see that they all contain a steroid backbone, but they di er in the type and position of substituents (functional groups) on the steroid backbone (Figure B25). It is these di erences that give the particular steroid its biological properties.
28 B HUMAN BIOCHEMISTRY CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

3

CH
17

CH2 C H2

H3C CH2 CH H3C CH3 CH3

progesterone

CH3

ketone

cholesterol

HO
hydroxyl alkene

O
ketone alkene

CH3 CH3

OH
hydroxyl benzene ring

CH3

OH
hydroxyl

testosterone

O
ketone alkene

HO
hydroxyl

Figure B25 Structures of cholesterol, progesterone, testosterone and oestradiol.

All contain a substituent at the C17 position, but in cholesterol it is a branched hydrocarbon chain, whereas in progesterone it is a ketone group, and in testosterone and oestradiol it is a hydroxyl group. Both progesterone and testosterone have a ketone group at C3, whereas oestradiol has a hydroxyl group (it is named thus as it contains two hydroxyls and hence is a diol). Cholesterol has a C=C in the B ring (see also Figure B22), whereas testosterone and progesterone have a C=C in the A ring and oestradiol has an aromatic A ring (a benzene ring). It is not surprising that all these steroids have similar structures, because oestradiol is biosynthesised from testosterone, which is in turn biosynthesised from progesterone, which is derived from cholesterol.

Oral contraceptives
There are di erent types of oral contraceptives probably the most commonly used is called the combined oral contraceptive pill, which contains a combination of oestrogen and progesterone. It works in a number of ways: it prevents the release of an egg from the ovary, i.e. it prevents ovulation from occurring; it makes the lining of the endometrium thinner so that it is unsuitable for implantation of a fertilised egg; and it makes the mucus in the cervix thicker to prevent sperm from reaching the egg. If taken correctly, the combined oral contraceptive pill can be more than 99% e ective at preventing pregnancy.

Steroid use and abuse

As mentioned above, steroids are used medically as oral contraceptives. They can also be used as hormone-replacement therapy (HRT) in women who are going through the menopause. In the menopause, the ovaries stop producing oestrogen, and so the level of oestrogen in the body drops dramatically. This leads to symptoms such as night sweats, sleeplessness and hot ushes. HRT replaces the hormones and thus alleviates the symptoms of the menopause. Because HRT contains oestrogen, its long-term use has been linked with an increase in the risk of breast cancer, as some types of
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011 B HUMAN BIOCHEMISTRY 29

breast cancer are dependent on oestrogen for their growth. Once HRT is stopped however, a womans risk of breast cancer starts to return to that of the general population within three years of stopping treatment. Other clinical uses of steroids include for the treatment of in ammation and associated conditions. Hydrocortisone (also known as cortisol) is a naturally occurring corticosteroid, so called because it is produced in the adrenal cortex in the adrenal glands (there are two adrenal glands in the body, one situated above each kidney). One of its e ects is to reduce in ammation, and therefore it, and synthetic corticosteroids, are used in the clinic for a variety of conditions, such as eczema, rheumatoid arthritis and asthma. It was mentioned earlier that testosterone is an androgen (a male sex hormone). It has uses medically as an androgen replacement in men who have testosterone de ciency, for example, because of a disorder of the testes. Androgens are also used non-medically, however for example, in sport. Androgen abuse is the use of androgens for non-medical purposes (they are called anabolic steroids because they promote tissue growth, in particular of muscle). The three most common anabolic steroids that are abused are testosterone and the synthetic derivatives nandrolone and stanozolol. They are taken by sportsmen and women to enhance performance, because they increase muscle mass and are also believed to improve endurance. They have been used in disciplines such as athletics, weightlifting and cycling. The ethical implications for taking anabolic steroids is clear, in that it gives that person an unfair advantage over their competitors and is thus cheating. It is a major concern to sporting bodies worldwide, and random drug screening in major sporting events is routinely employed to detect abuse. In the wider community, anabolic steroids are also used for bodybuilding and by a minority of people in certain occupations, such as security guards and bouncers, for cosmetic reasons to give themselves a more masculine and intimidating look. Abusing anabolic steroids can have a major impact on the body their use can cause a number of side e ects, such as breast growth in men, acne, infertility, mood swings and aggressiveness. They can also cause high blood pressure, liver disease (including cancer), heart attack or stroke. Psychologically, abusers of anabolic steroids can become addicted to them, developing an increased desire to keep taking them, even if unwanted side e ects occur.

Test yourself
15 Label the rings A, B, C and D and state how many ketone groups are present in this steroid.
H3C CH3 C CH3 O

30

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B7 Enzymes
Enzymes are proteins evolved by living organisms for the speci c function of catalysing biochemical reactions. They are found throughout the cell and catalyse virtually every conversion that occurs in the cell. Some enzymes are also found outside the cell for example, in the blood plasma. There are many types of enzyme, and each type has a name based on the type of reaction it catalyses and/or on the type of molecule on which it acts. For example, transferase enzymes catalyse transfer of a functional group, oxidoreductase enzymes catalyse oxidationreduction reactions, proteases break down proteins and lipases break down lipids. Note that the enzyme name ends in -ase; this is true for most enzymes. Enzymes are proteins, and their activity is dependent on their shape, i.e. their tertiary structure. A number of enzymes also have a quaternary structure, where they consist of two or more sub-units. Thus, quaternary structure is also important for the functioning of those enzymes. Enzymes act as biological catalysts they speed up biochemical reactions in the body without themselves undergoing any permanent chemical change. Most reactions catalysed by enzymes would not proceed to any signi cant extent without the presence of enzymes enzyme-catalysed reactions are typically 108 to 1012 times faster than the corresponding uncatalysed reactions. They speed up reactions by lowering the activation energy of the reaction; they do not make an unfavourable reaction favourable (see Chapter 6, page 250 of the Coursebook). They do this by providing an alternative pathway for the reaction, which has a lower activation energy. They also provide an area (the active site) for the reactants to come together and thus make it more likely that the reactants will react. The reactants involved in enzyme-catalysed reactions are called substrates, and enzymes are highly speci c for the particular substrate on which they act. Some enzymes act on only one substrate, whereas others act on a group of related substrates. The enzyme must bind temporarily to the substrate for the reaction to take place. This binding takes place in a mostly hydrophobic pocket called the active site. The active site is normally situated near the surface of the enzyme, towards one end of the protein. The active site is where catalysis takes place, and its shape is key to the speci city of the enzyme. The type and position of amino acids in the active site make it speci c for substrates of a certain size and shape. When a substrate (S) binds to the enzyme (E) active site, it forms a reaction intermediate known as an enzymesubstrate complex (ES). This is when the substrate enters the active site and forms interactions with R groups of amino acids in the active site. The type of binding is reversible, i.e. weak bonding such as hydrogen bonds, electrostatic interactions and van der Waals forces. Formation of the enzymesubstrate complex can cause the substrate molecule to become strained (distorted), and this will then more readily form the product (P), with regeneration of the enzyme. The product then di uses away from the enzyme active site, as it does not bind as e ectively
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

HL

Learning objectives

Describe the structure and function of enzymes as biological catalysts, including the mechanism of enzyme action, and proposed models for substrate binding Describe how enzyme activity changes with substrate concentration Determine Vmax and the Michaelis constant (Km) by graphical means and explain the importance of Km Explain how heavy metal ions, temperature changes and pH changes can a ect enzyme activity Compare the modes of action of competitive and noncompetitive inhibitors, including how they a ect Vmax and Km Describe the similarities and di erences between enzymes and inorganic catalysts

B HUMAN BIOCHEMISTRY

31

HL to the active site as the substrate. A general equation for the reaction is

given below: E+S

ES E + P

Enzyme speci city was rst compared to a key (the substrate) tting into a lock (the active site of the enzyme). This was called the lock-and-key hypothesis and it proposed that the active site was a complementary shape to the substrate, like a speci c key is a complementary shape to its lock (Figure B26). However, a more recent hypothesis proposes that for some enzymes, when the substrate enters the active site, it can cause a change in the shape of the active site to better accommodate the substrate, i.e. the active site changes to a shape complementary to the substrate only after the substrate has entered the active site. This is known as the induced- t hypothesis (Figure B27).

enzyme active site substrate

enzymesubstrate complex

Figure B26 The lock-and-key hypothesis.

enzyme substrate complex enzyme active site substrate enzyme active site changes shape slightly to accomodate substrate

Figure B27 The induced-t hypothesis.

Enzyme kinetics
A lot of work was carried out at the beginning of the 20th century to study the e ects of substrate concentration on enzyme activity. At low substrate concentrations, the rate of the enzyme-catalysed reaction is proportional to the substrate concentration. As the substrate concentration increases, however, the rate of reaction increases, but to a lesser extent, and is no longer proportional to substrate concentration. Then at high substrate concentrations, the rate of reaction remains constant and does not increase further with an increase in substrate concentration. This can be explained as follows: when the substrate is in low concentration, there is a su cient number of enzyme active sites available to bind substrate and form the ES complex, so as the substrate
32 B HUMAN BIOCHEMISTRY CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

concentration increases, more ES forms and the rate increases proportional HL to the increase in substrate concentration. The rate is essentially rst order with respect to the substrate. As the substrate concentration increases further, however, some of the active sites are already occupied with substrate and so there are not enough active sites to bind all of the substrate.This means that the rate of reaction increases less than would be expected when the substrate concentration increases.This results in a slowing down in the increase of the rate of reaction and the rate is now no longer proportional to the substrate concentration. When the substrate concentration is high, all of the active sites of the enzyme molecules are occupied by substrate, and so the rate of reaction remains constant (maximum rate), i.e. any further increase in substrate concentration results in no increase in rate of reaction, as the enzyme is saturated with substrate. The enzyme is working at maximum capacity as soon as an active site becomes vacant, it is occupied almost immediately by a substrate molecule. The rate is zero order with respect to the substrate when the substrate concentration is su ciently high. The curve produced is known as a MichaelisMenten curve (Figure B28), named after Leonor Michaelis and Maud Menten, who were pioneers in enzyme kinetics. Note from the curve that the rate for an enzyme saturated with substrate is known as the maximum velocity (Vmax). Vmax varies from one enzyme to another and is dependent on reaction conditions such as temperature and pH. Note also the Michaelis constant (Km). This is the concentration of substrate when the rate is equal to one half Vmax. Km is a useful constant, as it gives an indication of the a nity of an enzyme for a substrate, i.e. how well the enzyme binds the substrate (it is thus a measure of the stability of the ES complex). If an enzyme has a low Km, this indicates that it has a high a nity for a substrate, as only a small concentration of substrate is needed for the reaction to proceed at half its maximum velocity. Large Km values indicate that the enzyme has less a nity for the substrate, as a large concentration of substrate is needed to reach half Vmax.

Vmax maximum velocity for the reaction

Rate of reaction

1 2 Vmax

Km

Concentration of substrate

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

33

HL

Factors that inuence enzyme activity

Enzymes have evolved to work optimally under the conditions to which they are exposed in the body. If these conditions are changed signi cantly, this can have a dramatic e ect on the functioning of the enzyme. Three factors that can in uence enzyme activity are temperature, pH and the presence of heavy metal ions.

Temperature
Temperature has an e ect on enzymatic reactions (Figure B29): as the temperature increases, the kinetic energy of the system increases and there is more chance that substrates with energy greater than the activation energy will collide with the enzyme active site. Also, as the temperature increases, more collisions occur in a certain time between the enzyme and substrates. Therefore, increasing the temperature increases enzyme activity.

Rate of reaction

optimum temperature

denaturation occurs, leading to loss of enzyme activity

20

40 Temperature / C

60

Figure B29 The effect of temperature on enzyme activity.

This is true only up to a certain point if the temperature increases too much, the rate of the enzymatic reaction will decrease. This is because at higher temperatures, the kinetic energy (vibrations) of the enzyme will break the interactions that hold the enzyme, and thus the active site, in its speci c three-dimensional shape. As the shape of the active site is key to the activity of the enzyme, any change in shape will result in loss of functioning of that enzyme, as it will no longer be able to bind the substrate e ectively. The loss of the tertiary structure is known as denaturing.

pH
Enzymes work within a relatively narrow pH range, depending on the pH of their environment in the body. The optimum pH varies widely from one enzyme to another: for example, digestive enzymes such as pepsin, which act in the stomach, have an optimum pH of approximately 1.5 to 2.5, which is the pH that they would be exposed to in the stomach; however, digestive enzymes that act in the intestines, such as pancreatic lipase, have an optimum pH of approximately 8.
34 B HUMAN BIOCHEMISTRY CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

If the enzyme is exposed to a pH above or below its optimum pH, HL activity starts to decline. This is for two reasons: rstly, some enzymes contain ionisable amino acids at the active site that participate in the catalytic action of the enzyme; changes in the pH a ect the ionisation of those amino acids and thus in uence their ability to participate in the reaction. A second reason for the decline seen in enzyme activity is denaturation: signi cant changes in pH change the charges on the R groups of the amino acids that form the intramolecular interactions that dictate the shape of the active site. The resultant change in shape results in a loss of function of that enzyme, as described above for temperature.

The optimum temperature for enzymes in the human body is around 37 C, i.e. body temperature. Above that temperature, the enzyme starts to denature as bonds responsible for holding the protein in its threedimensional shape break.

The presence of heavy metal ions

Heavy metals such as silver (Ag+), mercury (Hg2+) and lead (Pb2+) have strong a nity for sulfhydryl (SH) groups they react with sulfur atoms of the sulfhydryl groups found in cysteine residues in the enzyme active site, replacing the hydrogen atom. The shape of the enzyme is thus altered if these cysteine residues are involved in forming interactions that contribute to the tertiary structure of the enzyme, as they are no longer able to do so. This is the mechanism by which these heavy metals are poisonous.

Enzyme inhibitors
If a chemical binds to an enzyme and prevents it from carrying out its catalytic activity, the enzyme is said to be inhibited, and the chemical is called an enzyme inhibitor. There are two main types of enzyme inhibitors, depending on where they interact with the enzyme: competitive inhibitors and non-competitive inhibitors. Enzyme inhibitors are widely used as medicinal drugs, the most common being the competitive inhibitors.

Competitive enzyme inhibitors

As their name suggests, competitive inhibitors compete with the natural substrate for binding to the enzyme they thus bind to the active site of the enzyme. Competitive inhibitors normally have a structure similar to the natural substrate this allows them to form interactions with the active site. Once the inhibitor enters the active site, it binds, forming an enzyme inhibitor complex (rather than an enzymesubstrate complex). The inhibitor is not acted on by the enzyme and so does not form products instead, it blocks the entry of the substrate and thus stops the enzyme from acting on the substrate and carrying out catalysis (Figure B30).

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

35

HL

Competitive inhibitors are usually reversible, so the enzymeinhibitor complex breaks down to release the inhibitor, which then leaves the active site. Because the inhibitor and substrate are competing for the active site, increasing the substrate concentration will make it more likely that the substrate will enter the active site, and thus inhibition will be reduced. The maximum velocity (Vmax) of the reaction will remain the same, but it will take a higher concentration of substrate to reach Vmax, so the Km will be higher (Figure B31).

Vmax

no inhibitor present Rate of reaction competitive inhibitor present

1 2 Vmax

Km

Km Substrate concentration

Figure B31 The effect of a competitive inhibitor on Vmax and Km.

Non-competitive inhibitors
Non-competitive inhibitors do not compete with the natural substrate, as they do not bind to the active site, but another region of the enzyme. This binding causes a conformational change in the shape of the active site, which prevents the substrate from binding (Figure B32). As the inhibitor does not compete with the substrate for the same site, increasing the substrate concentration does not reduce inhibition. This means that the Vmax is reduced in the presence of this type of inhibitor, but the Km is the same (Figure B33).

noncompetitive inhibitor

binding of inhibitor

active site substrate shape of active site changed so that substrate cannot bind

Figure B32 The mechanism of a non-competitive inhibitor.

36

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

HL
Vmax no inhibitor present Rate of reaction Vmax non-competitive inhibitor present

1 2 Vmax 1 2 Vmax

Km Substrate concentration

How do biological catalysts compare with inorganic catalysts?

Both enzymes and inorganic catalysts speed up reactions by providing an alternative pathway of lower activation energy. Neither changes the position of equilibrium or yield of the reaction. Enzymes are highly speci c for their substrate, whereas inorganic catalysts are often non-speci c and can catalyse several reactions. Enzymes have an optimum temperature and are denatured at high temperatures, whereas inorganic catalysts are much less a ected by the conditions and generally work well at high temperatures. Enzymes display saturation kinetics, i.e. reach a maximum velocity when substrate concentration is increased; most inorganic catalysts generally do not show saturation.

Test yourself
16 Enzyme X has a Km of 2.0 107 mol dm3 for a particular substrate, whereas enzyme Y has a Km of 2.0 106 mol dm3 for the same substrate. Which enzyme binds better to the substrate? 17 What types of interactions are possible between a competitive reversible inhibitor and the enzyme active site?

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

37

Learning objectives

HL

B8 Nucleic acids
As their names suggest, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are nucleic acids. DNA carries the genetic code of the organism. When cells divide (make copies of themselves), the DNA of the cell must be copied (called DNA replication) so that the new cells will have the same set of genetic information within them. When organisms reproduce, they copy their DNA and pass it on to the next generation. All organisms house their genetic information within DNA, except for some viruses, which use RNA.

Describe the structures of nucleotides and polynucleotides (nucleic acids) Describe the di erences in structure between DNA and RNA Explain the double helical structure of DNA Describe how DNA carries the genetic code, and explain how DNA directs protein synthesis Describe the steps involved in DNA pro ling and explain its role in criminal investigations and in paternity cases
O O P O

Structure of nucleic acids

Nucleic acids are polymers made up of monomers known as nucleotides. Nucleic acids are thus also called polynucleotides. Nucleotides consist of a ve-carbon (pentose) sugar, an organic nitrogen-containing heterocycle (N is part of the ring) called a base and a phosphate group (Figure B34). The pentose sugar is di erent in DNA and RNA. In RNA, the sugar is ribose, and in DNA, the sugar is 2-deoxyribose, as it lacks an oxygen at the C2 position (Figure B35).
HO HO

phosphate

pentose sugar

base

5' CH2 H H OH

OH O H 2' OH
ribose

5' CH2 H H OH

OH O H 2' H 1' H

O H 2' H

1' H

1' H

2-deoxyribose

Figure B34 The general structure of a nucleotide.

Note that we use the numbering C1 to C5 ( = prime) when talking about the sugar carbons in a nucleotide. This is because in nucleotides, the atoms of the base are numbered 1 to 6 (in pyrimidines) or 1 to 9 (in purines), and so to avoid confusion, the carbon atoms in the sugar are numbered C1 to C5.

The bases of nucleic acids are derivatives of either purine or pyrimidine (Figure B36) and are known as purines and pyrimidines. The purines that occur in nucleic acids are adenine (A) and guanine (G); the pyrimidines are cytosine (C), thymine (T, in DNA not RNA) and uracil (U, in RNA not DNA) (Figure B36). The base is bonded to the sugar at the C1' position of the sugar. The phosphate group in a nucleotide is usually attached to the oxygen of the C5' hydroxyl group of the pentose sugar. Nucleotides join together to form polynucleotides. The type of reaction is a condensation reaction between the phosphate attached to the C5' of one nucleotide and the hydroxyl group at C3' of another nucleotide. The nucleotides are thus joined covalently by a phosphodiester link (phosphate ester on both sides) between the sugars (Figure B37). Nucleic acids may consist of thousands of nucleotides linked together. RNA is a single strand of nucleotides, whereas DNA is a double strand. Each strand of nucleotides has a repeating sugarphosphatesugar phosphate backbone, and attached to each sugar is a base.

38

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

N N H

HL
N N
purine

N N
pyrimidine

Examiners tip You are not required to learn the structures of the nucleotide bases, but you should be able to recognise them.

NH2 N N H N N N N H

O NH N
guanine (G) purine bases

NH2

NH2 N N H
cytosine (C)

O H3C NH N H
thymine (T)

O NH O N H
uracil (U) pyrimidine bases

Figure B36 The structures of purines and pyrimidines found in DNA and RNA.

O N NH N NH2 H N N CH2 H H
3'

N O CH2 H H O O P O O H H O CH2 H H O
3' 5'

(G) O H H O

NH2

O (C) NH2

O P O

N N

N (A) O H H O
1'

O P O

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

39

HL

Differences between RNA and DNA

The di erences between DNA and RNA are summarised as follows: DNA is a double-stranded nucleic acid, whereas RNA is single stranded DNA contains thymine, whereas RNA contains uracil as a base DNA contains deoxyribose (no OH on C2') as the sugar, whereas RNA contains ribose.

Structure of DNA
Watson and Crick famously proposed the double-stranded structure of DNA in 1953. DNA is a double helix, consisting of two polynucleotide strands that spiral around an axis. Each complete turn of the helix is ten nucleotides in length. The sugar-phosphate backbone in each strand winds around the outside of the helix, with the nucleotide bases attached to the sugars stacked in the interior of the helix. The hydrophilic sugarphosphate backbone is thus exposed to the aqueous environment of the cell, while the relatively hydrophobic bases are shielded from this environment in the interior of the helix. Each of the bases on one strand forms hydrogen bonds with a base on the opposite strand. The bases pair together in a speci c way: the adenine bases on one strand form hydrogen bonds only with the thymine bases on the opposite strand (two hydrogen bonds) and the guanine bases on one strand hydrogen bond only with cytosine bases on the other strand (three hydrogen bonds). This speci c interacting of bases is known as base pairing, and the two bases involved are called base pairs (Figure B38). Each base pair consists of one purine base and one pyrimidine base. The structure of DNA has been likened to a ladder, which has been twisted into a helix. The base pairs are the rungs of the ladder, whereas the sugar-phosphate backbones are the sides of the ladder (Figure B39).

DNA carries the genetic code

The nucleus of the cell houses the chromosomes; in humans, there are 46 chromosomes per nucleus, made up two sets of 23 chromosomes, one set inherited from each parent. Chromosomes are long, coiled strands of DNA and proteins. The DNA in these chromosomes contains genes, which carry all the information needed for the individual to grow, live and reproduce. Genes are stretches of nucleotides in the DNA. Each gene has a speci c sequence of nucleotides. As the sugars and the phosphates within DNA are constant, it is the sequence of nucleotide bases that gives each gene its originality. When a cell divides, it needs to copy its DNA so that the new cell will have an identical set of chromosomes to the parent cell. The process of copying DNA is called DNA replication and involves unwinding and separating the two strands of DNA, accompanied by breaking the hydrogen bonds between the base pairs. This exposes the nucleotide bases of the DNA (which were in the interior of the helix) and allows the bases
40 B HUMAN BIOCHEMISTRY CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

P O H

base pairs

H H O H N N O N O N N H O H H N H N N N (C) H

H H O

H H2C

O P O H O

N N

O CH2 H H O O P O CH2 H H O
3'

N O H H O H

(G) H

N H N H H

H H O

N (G) N H3C H

H2C O

N N O H H O

P O H H

O (C)

H H

H N

N O

N (T)

H2C O
DNA strand

O P O CH2 H H O O P O

N (A) O H H O H

HL
hydrogen bonds

DNA strand

Figure B38 Complementary base pairing in DNA.

on each of the DNA strands to be used as a template for the formation of a complementary DNA strand (Figure B40). The formation of the new strands occurs by free nucleotides forming complementary base pairs with the DNA template strands: guanine nucleotides pair with cytosine bases on the DNA strand; thymine nucleotides pair with adenine bases on the DNA strand, and so on. The free nucleotides are joined together by phosphodiester links to form the new strands of DNA. So how do genes carry the code for life? To understand this, we need to know that each gene carries the code for the production of a single
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011 B HUMAN BIOCHEMISTRY 41

HL

parent strand

parent strand

A G A

C A C

G T

T C T
C A T

A G T C

A C T C G T G A G C T
A G

G A
T A A C G T C T G C

G G T C T A

C C
DNA strands separate

G A A

A T C G T
free nucleotides base-pair with bases on the parent DNA strand and are joined to the growing DNA daughter strand A pairs with T G pairs with C

Figure B39 The double-helix structure of DNA.

A G

T C

Remember that proteins are made up of a speci c sequence of amino acids (called the primary structure). This sequence gives the protein its shape and therefore its function, and it is the sequence of nucleotide bases within each gene that dictates the primary structure of the protein produced. In other words, the information for the structure of each protein is carried in the sequence of nucleotide bases within the particular gene.

T C
hydrogen bonds

A G

T C

A G

Figure B40 DNA replication.

Translation is the process of protein synthesis in which the code held in the sequence of bases of the mRNA is translated into the sequence of amino acids (primary structure) of the protein.
42 B HUMAN BIOCHEMISTRY

protein. It is these proteins produced by the cell that carry out the thousands of biochemical processes that are responsible for life. For a cell to produce a protein, the gene must rst undergo a process called transcription. This occurs in the nucleus, and the rst step in this process is the unwinding and separation of the two strands of DNA on which the gene is situated. In a similar manner to DNA replication, this exposes the nucleotide bases of the gene and allows the bases on one of the DNA strands to be used as a template. Transcription di ers to DNA replication, however, in that only one strand of DNA is used as a template and the complementary strand produced is a ribonucleic acid called messenger RNA (mRNA). The complementary strand of mRNA is built up through complementary RNA nucleotides (called ribonucleotides) forming base pairs with the exposed bases of the DNA template. Guanine pairs with cytosine and adenine pairs with uracil (not thymine, as in DNA). As each ribonucleotide comes in and forms a base pair, it is joined covalently to the growing mRNA chain by a phosphodiester link. This results in the production of a strand of mRNA that has the complementary sequence of bases to the gene of the DNA template strand. This mRNA then leaves the nucleus and enters the cytoplasm, where it takes part in the second process to produce a protein, known as translation.
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

During translation, the mRNA rst attaches to a ribosome (a small HL organelle in the cytoplasm) and the code is read by a type of RNA called transfer RNA (tRNA). tRNAs are small RNA molecules with an amino acid covalently attached to one region of the molecule. Another region of the same tRNA molecule interacts with complementary bases on the mRNA. The tRNA interacts with a sequence of three nucleotide bases on the mRNA; these three bases are called a triplet code, or codon, and the three complementary bases on the tRNA are called an anticodon. Each codon corresponds to only one amino acid, although several codons may correspond to the same amino acid. For example, the codon UUU on mRNA corresponds to the amino acid phenylalanine. By this, we mean that a tRNA molecule with the anticodon AAA (remember A base pairs with U) will have a phenylalanine amino acid covalently attached to it. The anticodon of tRNA will interact with the complementary codon on the mRNA and the phenylalanine amino acid will get incorporated into the growing polypeptide chain. The mRNA is read sequentially, so the next three bases (codon) will be exposed in the ribosome and then the complementary tRNA molecule bearing its speci c amino acid will interact with it, incorporating the amino acid into the polypeptide chain. And so on, and so on (Figure B41). Thus we can now see how the sequence of bases in the DNA dictates the sequence of amino acids in the protein synthesised.

amino acid

tRNA

mRNA b

DNA proling
DNA pro ling is a method used to identify individuals by di erences in their DNA. It is used to identify criminals or exonerate suspects in criminal cases, as well as to determine whether certain people are related, for example in paternity cases, where there is a dispute over who is the father of a child. DNA pro ling does not look at the whole of an individuals DNA, as only a small percentage of the DNA varies between individuals. The method looks at regions of the DNA that show high variability among individuals. These are non-coding regions of DNA: stretches of nucleotide bases that do not code for any protein. In these non-coding regions are areas known as short tandem repeats (STRs), which are nucleotide base-pair sequences (of about three to ve base pairs in length) that repeat over and over again in a region (known as a locus) of the chromosome (e.g. ACTACTACTACTACTACT). The number of times this sequence of bases (ACT in this case) repeats varies between individuals. DNA pro ling analyses samples of DNA from a number of loci on the chromosomes (usually ten STR samples from ten di erent chromosomes). This builds up a DNA pro le for that individual. Statistically, no two people are likely to have the same number of repeats in all of the STRs looked at (except identical twins), and hence this pro le is as unique as a ngerprint. DNA pro ling is commonly known as DNA ngerprinting. The procedure rst involves isolation of the DNA from the sample source. In the case of DNA pro ling in forensic cases, the source can be blood, semen, skin cells, hair or saliva (e.g. from a cigarette butt) found at the scene of a crime, or it can be a blood sample taken from a suspect (to compare the DNA).

Figure B41 The process of translation. (a) Two tRNA molecules interacting with the codons on the mRNA. When the second tRNA molecule (bearing the blue amino acid) comes in and interacts with the mRNA, the growing polypeptide chain is cleaved from the rst tRNA molecule and joined to the amino acid on the second tRNA molecule. (b) The rst tRNA molecule then leaves and a new tRNA molecule will come in and interact with the next codon on the mRNA chain. The polypeptide chain will then be joined to the amino acid on this new tRNA molecule, and so on, and so on, until the complete polypeptide chain has been produced.

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

43

HL

Figure B42 A DNA prole.

The isolated DNA is cut into small pieces using restriction enzymes that recognise speci c base sequences in the STR regions of the DNA. These enzymes act like a pair of scissors, chopping up the DNA at those particular sequences. Multiple copies of these STR regions are then produced using a technique known as polymerase chain reaction (PCR). PCR uses a DNA primer (to initiate DNA replication) and a DNA polymerase enzyme (to polymerise nucleotides to produce new complementary strands of DNA). In this way, thousands or millions of copies of the DNA fragments may be produced. These DNA fragments are then separated according to size using gel electrophoresis. DNA bears a negative charge (owing to the phosphate groups), and DNA fragments thus move towards the positive electrode when an electric eld is applied. Smaller fragments move faster than larger fragments, and thus move further down the gel sheet. The resulting pattern of bands is then transferred to a nylon membrane, and a radioactive label such as 32P is then added, which combines with particular bands of the DNA. X-ray lm is then exposed to the radiation produced by the 32P and developed the DNA fragments appear as dark bands on the lm (Figure B42). The pattern of the bands is unique to a particular individual, and so this pattern is compared to the DNA patterns of the suspect(s) to see if there is a match. DNA pro ling can also be used in paternity cases, where the DNA patterns are compared to see if there are signi cant matches between child and proposed father. Half of the childs genetic material is from the father, so half of the DNA fragment bands of the child should match those of the father (the other half should match those of the mother).

Test yourself
18 Name the only nucleotide base that does not contain an amide functional group. 19 Which nucleotide base complementary base pairs with guanine and how many hydrogen bonds form between the two bases?

Learning objectives

B9 Cellular respiration
Organisms need energy to carry out the thousands of biochemical processes that maintain life. Humans derive their energy from food: glucose from carbohydrate and fatty acids from fats, for example, are broken down in the cell in a series of reactions that yield energy in the form of a molecule called ATP. This ATP is then used to fuel cellular reactions, such as protein synthesis, and many other enzyme-catalysed processes that occur in the cell. There are two ways that these food molecules can generate energy, called aerobic and anaerobic respiration. Aerobic respiration results in the production of more ATP than anaerobic respiration and thus yields more energy. Aerobic respiration involves oxygen. Therefore it is carried out when oxygen is present. The process involves the oxidation of food
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

Compare the processes of aerobic and anaerobic respiration, highlighting the redox reactions involved and the energy released Describe the role of copper ions (in cytochromes) in electron transport and iron ions (in haemoglobin) in oxygen transport

44

B HUMAN BIOCHEMISTRY

molecules, such as glucose, to produce carbon dioxide, water and energy (in the form of ATP). General equation: C6H12O6 + 6O2 6CO2 + 6H2O + energy The rst step in the breakdown of glucose is common to both aerobic and anaerobic respiration and involves a series of reactions known as glycolysis.

HL

Glycolysis
Glycolysis involves the breakdown of the six-carbon sugar glucose to two three-carbon molecules called pyruvate. This process occurs in the cytosol (intracellular uid) of the cell and does not require oxygen. There are ten enzyme-catalysed steps involved in the production of pyruvate, but the overall reaction can be simpli ed:
H3C C6H12O6 2

O C C

glucose

pyruvate

During glycolysis, the glucose molecule undergoes oxidation (loss of electrons) to yield pyruvate (the average oxidation number of C in glucose is 0 but it is +2 in pyruvate); the coenzyme nicotinamide adenine 3 dinucleotide (NAD+) gets reduced to NADH in the process. The process of glycolysis uses up two molecules of ATP for every glucose molecule converted to pyruvate; however, four molecules of ATP are generated, so there is a net production of two ATP molecules. The fate of pyruvate is di erent depending on whether oxygen is present or not. Under anaerobic conditions (where oxygen is not available), the pyruvate is reduced. In humans, for example in muscle cells during exercise, oxygen becomes in short supply and there is not enough to keep up with the demands of the cell; in this case, the pyruvate is reduced to lactate (the average oxidation number of C in lactate is 0). NADH is oxidised in the process to NAD+.
H H H C H
pyruvate

A coenzyme is an organic molecule needed by an enzyme to be fully active.

The average oxidation number of C is worked out by assuming that O has an oxidation number of 2 and H of +1.

O C C

O + NADH + H O
+

H H C H

O C H
lactate

O C + NAD+ O H H C O C C O + H+

H H C H

O C H + CO2

O In microorganisms such as yeast, anaerobic conditions resultHin pyruvate being reduced to ethanol (average oxidation number of C is 2 in pyruvate ethanol) and carbon dioxide. This occurs in two stages: H H C H
pyruvate

ethanal

H O C C O + H+ O H H C H
ethanal

O C H + CO2 H

H C H

O C H + NADH + H+ H

H C H

O C H H + NAD+

ethanal

ethanol

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

H O H O

B HUMAN BIOCHEMISTRY

45

HL

This is the basis of fermentation and the overall reaction starting from glucose is: C6H12O6 2C2H5OH + 2CO2
glucose ethanol

A brief, simpli ed summary of aerobic respiration. 1 Glucose is converted to two molecules of pyruvate during glycolysis. 2 Pyruvate undergoes a series of reactions, including entry into the citric acid (Krebs) cycle and is oxidised to CO2. During the oxidation steps, NAD+ becomes reduced to NADH. 3 The reduced coenzymes enter the electron transport chain, which consists of a system (chain) of protein complexes found in the inner membrane of the mitochondria. These proteins accept the electrons from NADH and pass them along the chain to the terminal electron acceptor, molecular oxygen, which is reduced to water.

This process does not yield any ATP; however, it does serve to convert NADH back to NAD+, which can then be fed back into glycolysis. Once NAD+ has been regenerated, glycolysis can continue. As glycolysis results in a net production of only two molecules of ATP, anaerobic respiration yields only a small amount of energy compared with aerobic respiration, which yields 36 molecules of ATP per molecule of glucose. Under aerobic conditions, pyruvate enters the mitochondria (rodshaped organelles, in which most of the energy is produced in the cell). Through a complex series of reactions and steps, pyruvate is ultimately oxidised to carbon dioxide, while oxygen is reduced to water.

The electron transport chain

It is the electron transport chain that generates the largest amount of ATP molecules. This is a series of proteins in the inner mitochondrial membrane that act as electron carriers, passing electrons from reduced coenzymes along the chain to molecular oxygen. It consists of a series of redox reactions, involving the ow of electrons from a reducing agent to an oxidising agent. The electrons ow along the chain in the direction of increasing electrode potential (reduction potential), i.e., passed from a stronger reducing agent to a stronger oxidising agent, with the ultimate reduction of oxygen to water (Figure B43).
strongest reducing agent strongest oxidising agent

electron transport chain

O2 e H2O

Figure B43 Representation of the electron transport chain.

The NADH coenzymes are strong reducing agents and give up their two electrons to the rst protein complex in the chain. They are oxidised back to NAD+ for reuse, and hydrogen ions (H+) are generated in this process. The electrons are passed on to an electron carrier (which accepts the electrons, i.e. gets reduced) and passes them on to the next protein complex along the chain until the terminal oxidising agent (O2) is reached. The equation for the reduction of oxygen is as follows: O2 + 4e + 4H+ 2H2O As the electrons are passed from one carrier to the next, hydrogen ions are pumped into the space between the inner and outer mitochondrial membranes. When the hydrogen ions ow back through the membrane (via a protein channel), energy is released, which drives the synthesis of ATP.

Electron carriers
Many of the proteins in the electron transport chain are cytochromes. Cytochromes act as electron carriers; they contain a prosthetic (nonprotein) group called a porphyrin, which is a large ring structure
46 B HUMAN BIOCHEMISTRY CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

consisting of four rings linked together. Most porphyrins have Fe at their HL centre, in which case it is known as a haem group (heme in the USA). Some cytochromes, such as cytochrome oxidase (the enzyme that reduces oxygen to water in the electron transport chain), also contain Cu. When cytochrome oxidase accepts electrons from the preceding electron carrier in the chain (which acts as a reducing agent and gets oxidised), the Fe and Cu change their oxidation states: Cu2+ is reduced to Cu+ (Cu2+ + e Cu+) Fe3+ is reduced to Fe2+ (Fe3+ + e Fe2+) Cytochrome oxidase now acts as a reducing agent and gets oxidised: it passes the electrons on to the terminal electron acceptor, oxygen, which is reduced to water: Cu+ is oxidised to Cu2+ (Cu+ Cu2+ + e) Fe2+ is oxidised to Fe3+ (Fe2+ Fe3+ + e) Electrons transferred to oxygen: O2 + 4e + 4H+ 2H2O

Oxygen carriers
As well as transporting electrons, haem-containing proteins also play an essential role in transporting oxygen: haemoglobin transports oxygen from the lungs through the bloodstream and releases it to the cells of the tissues, to carry out respiration. Haemoglobin consists of four polypeptide sub-units, each of which contains a haem prosthetic group with the iron at the centre of the haem in the Fe2+ oxidation state (Figure B44). Each haem can carry one
CH2 H3C CH

H3C

HC N N Fe N HC
2+

CH

CH3

N CH CH CH2

CH3

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

47

HL molecule of oxygen; therefore, each haemoglobin molecule can transport

four molecules of oxygen. Oxygen binds to haemoglobin reversibly.The haem Fe can bond to six ligands. In the unbound state, the Fe2+ is bonded to ve ligands: four ligands are the pyrrole nitrogens of the porphyrin and one ligand is an amino acid that attaches it to the protein.When molecular oxygen binds, this becomes the sixth ligand, and haemoglobin is said to be oxygenated (it is this oxygenated form that gives blood its red colour, owing to the red colour of the haem prosthetic group). In haemoglobin, the oxygen only binds reversibly, allowing its release to tissue cells, to be used in cellular respiration.

Test yourself
20 Use oxidation numbers to deduce whether the conversion shown below involves oxidation or reduction or both:
H H C H
pyruvate

O C C

O + H+ O

H H C H

O C H + CO2

ethanal

Exam-style questions
1 The energy value of foods can be obtained using a food (bomb) calorimeter. A 2.6 g sample of salmon was burnt in a food calorimeter containing 250 g water. It raised the temperature of the water from 20.4 C to 26.0 C. The speci c heat capacity of water is 4.18 J g1 K1. a How much energy (in kJ) is contained in 250 g of salmon? b Give one reason why the result obtained was not completely accurate. 2 Immunoglobulin G is an antibody that plays an important role in the immune system. It is a protein made up of four polypeptide sub-units. a The polypeptides in immunoglobulin G are made up from 2-amino acids. i Give the general structural formula for 2-amino acids. ii Describe two other characteristic properties of 2-amino acids. b Explain what is meant by the primary structure of a polypeptide chain and name the type of bond that links the amino acids together in the primary structure. c i Draw the structural formula of one of the dipeptides formed when glycine reacts with cysteine (structures are given in the IBO Chemistry Data booklet) and name the type of reaction occurring. ii Explain why it is possible to form more than one dipeptide when glycine reacts with cysteine. [1] [2] [2] [2] [2] [2] [2] [1]

d How many possible tripeptides could be produced by reacting glycine, cysteine and serine? Draw one of these tripeptides. e The amino acids in the immunoglobulin can be analysed using paper chromatography. i Why is the immunoglobulin rst treated with dilute hydrochloric acid before paper chromatography is carried out? ii Describe how paper chromatography is used to analyse amino acids.

[1] [4]

48

B HUMAN BIOCHEMISTRY

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

3 Carbohydrates are the most abundant class of biological molecules and include simple sugars as well as complex polysaccharides. a Glucose is the monosaccharide that makes up starch; draw its straight-chain structure. b Glucose can form two cyclic isomers. Explain why this occurs and name both isomers. c Name the two di erent types of polysaccharides found in starch and name the types of linkages that join the glucose units together in each form. d State the type of reaction that occurs when two glucose units join together to form a disaccharide and name the other product of the reaction. e Cellulose is also a polysaccharide made up of glucose units. Explain why humans, and most other animals, cannot digest cellulose. 4 Lipids play important roles in the body. a i De ne the term iodine number. ii If 11.43 g of I2 reacts with 0.015 mol of a fatty acid, explain what can be deduced about the structure of this fatty acid (Mr for I2 = 253.8 g mol1). [1] [3] [3] [3] [3] [3] [1] [3] [3] [2] [2]

b Write an equation to represent the reaction between fatty acids and glycerol to produce a triglyceride (the hydrocarbon chains can be represented by R). c Explain how the composition of fatty acids in fats and oils a ects their melting point. d Explain what an omega-3 fatty acid is and why an adequate dietary intake is important. e State one role of cholesterol in the body and describe how it is transported through the body. 5 a The structures of ascorbic acid (vitamin C) and retinol (vitamin A) are shown below. Explain whether they are fat- or water-soluble vitamins.
CH2OH HO H HO CH O O

[2]

OH

ascorbic acid (vitamin C)

H3C

CH3

CH3 H C C H C C H H C C H

CH3 C H CH2OH

CH3

retinol (vitamin A)

b Describe the e ect of a de ciency of vitamin A and suggest two possible solutions to overcome the problem.

[3]

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

B HUMAN BIOCHEMISTRY

49

6 Hormones are chemical messengers. a Name the characteristic structural feature found in the sex hormones, testosterone and oestradiol (structures are given in the IBO Chemistry Data booklet). b Identify two di erences in the structures of testosterone and oestradiol, with respect to functional groups. c Describe how the combined oral contraceptive pill prevents pregnancy. d State where the hormone insulin is produced in the body and describe its main e ect on the body.
HL 7 Enzymes catalyse almost every biochemical reaction in the body.

[1] [2] [2] [2]

a Describe, in general terms, how enzymes catalyse biochemical reactions. b Many medicinal drugs act by inhibiting enzymes in the body, either non-competitively or, more commonly, competitively. i Describe how competitive inhibitors work and how these di er from non-competitive inhibitors. ii What e ect does increasing the substrate concentration have on each type of inhibitor? iii How does each type of inhibitor a ect the Vmax and Km? c Describe two di erences between enzymes and inorganic catalysts. 8 a The structures of four nucleotide bases are given below. Draw the two sets of base pairs that are found in DNA, including the hydrogen bonds that form between them.
N HN N N
guanine (G)

[3]

[2] [2] [2] [2]

[3]

O N N H HN H N

H N N H

H O H N NH O
thymine (T)

CH3

N N NH O
cytosine (C)

b State two structural di erences between DNA and RNA. 9 Cytochrome oxidase is an enzyme involved in aerobic respiration. Describe the role played by cytochrome oxidase in aerobic respiration, including the role of the copper ions. Use suitable equations to illustrate your answer.

[2]

[5]

50

B HUMAN BIOCHEMISTRY