Module 1 Unit 5 Bio Chemistry

7/29/2019 Module 1 Unit 5 Bio Chemistry

1/66

Unit 5

Society ofCosmetic Scientists

Distance Learning

Module 1 Unit 5Bio Chemistry

Prepared by David Peers withGrace Abamba, Angela Beattie, David Benzies,Rachel Benzies and Brian Knight

To move through this unit,select the buttons shown onthe screen that look like this.

Reading from the left, theywill take you to:First Page (i.e. this screen),Previous Page, Next Page,Last Page, Previous View,Next View.

To jump to a topic, click here:

Contents

To jump to a section, click onits page number.


2/66

CONTENTS

1 Bio chemical Materials Carbohydrates 41.1 Introduction 41.2 Basic Carbohydrates 4Activity 1 Structure of simple carbohydrates 51.3 Bigger Molecules 6

Activity 2 Hemose Sugars 7Activity 3 Ring Structures of Sugars 81.4 More Complex Carbohydrates 9Activity 4 More Complex Sugars 91.5 Polysaccharides 101.6 More Complex Polysaccharides 121.7 Uses of Carbohydrates 12i) Energy Supply 12ii) Structural 12iii) Water Trapping 131.8 Summary 13Checklist 14

2 Lipids 152.1 Introduction 152.2 Biological fats and oils 152.3 The nature of fatty acids 152.4 The implications of unsaturation 17Activity 5 Double Bonds in Hydrocarbon Chains 172.5 Other classes of Lipids 19Activity 6 Comparison of Lipid Structures 202.6 Uses of Lipids 212.7 Summary 22Checklist 22

Appendix 1 23

3 Proteins 253.1 Introduction 253.2 Amino Acids 25Activity 7 Optical Isomers of Amino Acids 25Activity 8 Influence of Amino Acid Sidechains 283.3 Peptides 29Activity 9 Formation of a Tripetude 303.4 Proteins 323.5 Protein Structure 323.6 Tertiary Structure 35

3.7 Forces Invloved in Maintaining Tertiary Structure 363.8 Quaternary Structure 38Activity 10 Levels of Protein Structure 403.9 Summary 40Checklist 41

DIPLOMA/CERTIFICATE IN COSMETIC SCIENCE MODULE 1 UNIT 5

2 BIO CHEMISTRY


3/66

4 Enzymes 424.1 Introduction 424.2 Function of Enzymes 424.3 Enzyme Classification 43Activity 11 Classification of Enzymes 434.4 Enzyme Structure 444.5 The Enzyme Substrate Complex 44

Activity 12 Enzyme Structure and Mechanism 454.6 Enzyme Inhibition 471) Irreversible Inhibitors 472) Reversable Inhibitors 47Activity 13 Effect of Different Inhibitors 474.7 Summary 49Checklist 49

5 Metabolic Pathways 505.1 Introduction 50

6 Genetics and Cell Replication 526.1 Introduction 526.2 The Structure of DNA 52Activity 14 Base Structure of DNA 54Activity 15 The Principle of Complementary Base Pairs in DNA 56Checklist 576.3 Replication of DNA 57Activity 16 The Semi-Conservative Process of DNA Replication 586.4 DNA Transcription 58Activity 17 Processes Involving DNA and RNA 616.5 Summary 61Checklist 62

Appendix 2 63

Appendix 3 64

Appendix 4 65


3 BIO CHEMISTRY


4/66

1 BIO CHEMICAL MATERIALS CARBOHYDRATES

1.1 IntroductionBio chemistry involves thousands of different chemical compounds, which can be sorted into anumber of classes. Their application to Cosmetic Science is that these are the substances whichmake up human bodies. These are the substances to which cosmetic products are applied. Manyof them are substances from which cosmetic products are manufactured, as will be explained

during the Course. As this is an introductory unit, the basic nature of these substances will betreated in a more biological context, that of food. This treatment explains the ways in which theunderlying arrangements of chemical structure, often simply physical size and shape, underlietheir properties in real, everyday practice. In the next three sections, we will examine thestructures and properties of three major classes of bio chemical molecules, carbohydrates, lipidsand proteins. Make sure you have available your molecular model kit, provided in the PracticalActivity Kit.

1.2 Basic carbohydratesAs the first group of bio chemical substances to be considered, these will be discussed in somedepth. Many are used in the cosmetics industry, for example, modified celluloses are commonthickening agents. The basic principles established here, that underlying structures and patternsof bonding influence the properties of realsubstances, will then be applied to other materials,such as oils and proteins.

Carbohydrates contain the chemical elements carbon, hydrogen and oxygen. In the overallmolecular formula there are always twice the number of hydrogen atoms as there are oxygenatoms. For example, the carbohydrate substance which is most familiar in everyday life isprobably table sugar sucrose. It has the overall formula C12H22O11.

Actually, in general bio chemical terms, sucrose is something of an irrelevance. It is onlyimportant to sugar beet plants, sugar cane plants and humans. To a biologist, the word sugartends to meanglucose, C6H12O6, and this is the example that is given first in most textbooks.Why do you think that, other than perversity, I chose sucrose? One reason is its familiarity. Theaverage consumption in Britain is currently 110 g/day per head, giving a yearly total for the UK

of 2.2 million tonnes. (Source: Sugar Bureau.) And, if you think you dont eat that much, thereare 9 teaspoons (45 grams) in a can of soft drink. If you are not eating this much, somebody isgetting more than their fair share. And this is simply refined sucrose. There are many othersources of sugars. More pertinent, in my experience, is the fact that people who meet theformula for glucose first develop the lasting fixation that the number of carbon atoms in themolecule of carbohydrate must equal the number of oxygen atoms. Look at the formula forsucrose and count the different atoms: C12H22O11.

From this you can see that any carbohydrate will fit a general formula, CxH2yOy, where x and ycan be any number from 3 to several thousands. (Put this slightly differently, C x(H2O)y, and youhave carbon hydrate.)

The smallest, simplest sugars have 3 carbon atoms and are therefore called trioses. We shallexplore the possibilities of various arrangements of their components, since the principles alsoapply to more complicated examples. From our definition of the proportions of the chemicalelements found in carbohydrates, each of the three carbon atoms must be attached to theelements of water: H- and -OH.


4 BIO CHEMISTRY


5/66

ACTIVITY 1 Structure of simple carbohydrates(Allow about 15 minutes)

I am going to ask you to assemble molecular models, in order to explore the variousarrangements that are possible using the elements of a simple carbohydrate and which qualify ascarbohydrates. In doing so, I hope you will begin to understand how the molecular structuresand their physical shapes influence their properties. The principles you derive from assemblingthese models will be extremely useful later in the course and in your future work.

1) Assemble a chain of three carbons (black). Add to each the elements of water, hydrogen(white) and hydroxyl (white for hydrogen and red for oxygen).

If you were to write a structural formula for the molecule that you have constructed it wouldlook like this:

Unfortunately, as a molecular structure, this will not do because we have two spare bondsunfilled. The solution would seem to be to simply plug them with hydrogen atoms. This still willnot do. By adding more hydrogens, we have deviated from our basic criteria. (However, do notdismiss this new molecule. It represents a real substance, which we shall meet again.It is glycerol.)

2) Rearrange our first molecular structure, as shown above, containing the atoms C3H6O3 toproduce viable molecules, with each element showing its correct valency (carbon 4, hydrogen l

and oxygen 2). Those two spare bonds must be accounted for, in some way.

Do this now and draw structural formulae for your suggestions below. If this causes you anyhesitation, then you really should go back and work through Unit 1, Basic Chemistry. (Productionof double bonds will involve bending the bonds in your molecular model kit.)


5 BIO CHEMISTRY

C

C

C O

O

O H

H

HH

H

H


6/66

There are several possibilities. I have reproduced two in figure 1.

Figure 1. Possible arrangements of 3C: 6H: 3O

The first is known as an aldose sugar., because its carbonylgroup (-C=O) is on the end of themolecule as part of an aldehyde group.

The second is known as a ketose sugar, because -C=O is in the middle of the molecule as part ofa ketone group.

Both arrangements are trioses. They represent the simplest examples of two families of sugars.

They are isomers of each other. If you are not convinced that this sleight of hand representsdifferent chemical substances, think of typical, day-today examples. Aldehydes provide many ofthe off-flavours and smells in old foods think of the smell of over-ripe apples. The best knownketone is acetone, nail varnish remover. These are obviously different substances.

These two triose sugars are not met in everyday life and do not have common names. However,they are important in the pathways of chemical reactions which make up our metabolism andwe shall meet them again in later sections. Most sugars also display other forms of isometry,geometricand optical(orstereo) isometry. We dont need to worry about this at the moment.

We can now represent the chemical formula for a simple sugar as a chain of carbon atoms, mostcarrying the elements of water. One carbon atom will have a carbonylgroup (-C=O), either on

the end of the molecule (aldehyde) or in the middle (ketone), giving rise to two families ofsugars, the aldoses and the ketoses.

1.3 Bigger moleculesIf you go back to your original molecular model structure, you can see that we can still meet ourcriteria for a carbohydrate even if we insert more and more sets of

into our theoretical structure. This would give us larger molecules of sugars, tetroses (with fourcarbon atoms),pentoses (with five) and so on. The important ones, for now, are the hexoses

(with six carbon atoms). In these larger molecules, even more variations in arrangement arepossible. On the following page, in figure 2, I have drawn the two most important versions ofa hexose.


6 BIO CHEMISTRY

Aldehydegroup

Carbonylgroup

C

C

C

O

OHH

H

H OH

H

CC

C

OHOH

H O

H

H

H

C O

Ketose sugar

Ketonegroup

Aldose sugar

CH O

C O

C OHH


7/66

Figure 2. Structure of hexose sugars

The numbering system for the carbon atoms is conventional, counting from the end nearest tothe carbon atom which carries the most reactive functional group, in this case the carbonyl-C=O, towards the top of the formula in figure 9; carbon atoms l and 2 respectively.

ACTIVITY 2 Hexose sugars(Allow about 3 minutes)

a) Add up the numbers of different atoms in both glucose and fructose and write them below.

Both are C6H12O. They are isomers of each other.

b) Assemble a molecular model of glucose. Make sure that you have all the groups in the correctorientation. In the written formula, the hydroxyl group on carbon number 3 points the oppositeway. Make sure that this is reflected in your model. This is geometric isometry.


7 BIO CHEMISTRY

C

C

C

C

CHO

H

H

H

OH

HO

HO

HO

H

CH2OH

Carbon atomnumber

C

C

C

C

C

OH

H

OH

OH

HO

H

C

H O

H

H

H

H

OH

Glucose:an aldo-hexose

Fructose:a keto-hexose

Unspecificrepresentation(no informationon structure)

1

3

2

4

5

6

C

C

C

C

C

O

H

OH

OH

HO

H

C

H

H OH

H

H

OH

H

Number of atoms present

Carbon Hydrogen Oxygen

Glucose

Fructose


8/66

These open chain formulae for sugars have been useful in showing us that carbohydratemolecules have basic similarities that can be adapted to give a variety of substances. They arecalled Fischer structures, after the nineteenth-century chemist who was a pioneer incarbohydrate chemistry. Look at your molecular model of glucose, the sugar! You can see thatthe flat, unexciting depiction on paper represents a real collection of material substance. It wouldbe long and floppy. In a solution, buffeted by surrounding water molecules, it would twist about.Chemical bonds are of precise length and angle. In practice, the aldehyde group, on carbon

number l, would come close enough to the hydroxyl on the fifth carbon atom in the chain tointeract with it. A ring structure is formed (the Fischer formulae have been tightened up):

A better way of showing the ring is shown in figure 3. (The numbers reflect the carbon atoms,counting from what would have been carbon number l in the open chain structure, that is thecarbon atom carrying the most chemically reactive group, the aldehyde.)

Figure 3. Glucose as a ring structure

ACTIVITY 3 Ring structures of sugars(Allow about 3 minutes)

Adapt your molecular model into the ring format shown in figure 10.

Again, make sure that you have the correct orientation for all groups.

In forming this ring structure and handling your completed model, you will have a better senseof a three-dimensional substance. It has been estimated that more than 99% of glucosemolecules in solution are in such ring forms.


8 BIO CHEMISTRY

CHO

HCOH

HOCH

HCOH

HCOH

H2COH

HCOH

HCOH

HOCH

HCOH

HC

H2COH

O

4C

O

1C

2C3C

C

5

6 CH2OH

OHOH

HO

H

HH

H

OH

H


9/66

What would a fructose molecule look like in a ring form? Once again, the most reactive group isthe carbonyl, in this case being a ketone on carbon number 2. Once again, it reacts with carbonnumber 5, giving, in this case a five-membered ring, with two offshoots, as shown in figure 4.

Figure 4. Fructose as a ring structure

1.4 More complex carbohydrates

ACTIVITY 4 More complex sugars(Allow about 5 minutes)

Earlier, I said that the basic principles for production of a molecule of carbohydrate could beextended to produce larger and more complex molecules. Now, the ring structures, producedin Activity 9, will be combined to form even more complex sugars. Take your ring structurefor a molecule of glucose, construct another copy and align them as shown below:

If we remove the elements of water, shown shaded above, joining the two molecules, we have aparticular class of chemical reaction. (It is called condensation. The reverse, splitting a larger

molecule with insertion of water, is called hydrolysis.) This gives us the condensed sugar shownin figure 5.


9 BIO CHEMISTRY

5C

O

2C

3C4C

6CH2OH

1CH2OH

OH

H

H HOH

OH

4C

O

1C

2C3C

C

5

6 CH2OH

OHOH

HO

H

H H H

OH

H4C

O

1C

2C3C

C

5

6 CH2OH

OHOH

HO

H

H H H

OH

H


10/66

Figure 5. Condensed sugars

You have assembled an example of a disaccharide, formed by joining two monosaccharides. (It isworth emphasising that saccharins (artificial sweeteners) have no chemical relationship tosugars.) A number of disaccharides are significant in day-to-day life. The one we haveconstructed by combining two units of glucose is called maltose but others are possible asillustrated below:

GLUCOSE + GLUCOSE gives MALTOSE

GLUCOSE + FRUCOSE gives SUCROSE

GLUCOSE + GALACTOSE gives LACTOSE (milk sugar)

Look again at your model or the formula. We still have an hydroxyl group attached to a carbonnumber l on one end of the molecule and an hydroxyl group attached to a carbon number 4 atthe other end of the molecule. If we line up yet another glucose molecule, we can carry outanother condensation, to give a trisaccharide.

This can be repeated many times to give apolysaccharide.

1.5 PolysaccharidesThere are several variations we can create simply by combining glucose molecules in differingways. The one we have just created, a long wavy chain made up of 200- 300 glucose subunits

joined by 1-4 bonds, is called amylose. There are other possibilities. Look back at a glucosemolecule. There are 5 hydroxyl groups sticking out from the ring. Those on carbons number 1and 4 are the most likely to react together, because they are sticking out at the ends. As themolecules jostle around in solution in water, they are simply the hydroxyl groups which are mostlikely to bang into each other, giving the possibility of a chemical reaction. However, othergroups can also react. One possibility is shown in figure 6.

Figure 6. Alternative possibility for linking glucose molecules


10 BIO CHEMISTRY

O

CH2OH

H H

H

OH

OH

H

H

O

H

H

OH

OHHO

H

HH

CH2OH

O

OH

O

CH2OH

H

H

H OH

H

H

HO

HO

HO

H

H

OH

OHHO

H

HH

CH2OH

O

OH

disaccharide

O

H

H

H

O

HO

HO

H

CH2OH

HO OH

HOH

H

HO

CH2H

H

H

O


11/66

There is the possibility of a 1-6 bond. This produces a molecule which consists of chains ofglucose units, joined by 1-4 bonds, as in amylose above. About every twenty five glucose units, a1-6 bond starts a branch, giving the sort of pattern illustrated in figure 7:

Figure 7. Branching arrangement of polysaccharide chains

This molecule is called amylopectin. Amylose and amylopectin are not household names, butstarch is a mixture of the two. Starch from the wheat plant (flour) consists of about one thirdamylose and two thirds amylopectin. We have seen that different shapes and alignments enablemolecules to interact in various ways. Amylose is a loose, floppy chain, so a starch with a higherproportion of this would be looser; potato starch is an example. Amylopectin is a more compactmolecule, more of this gives the waxy starches, such as from peas.

It is easy to start thinking of these molecules as abstractions. Notice again how their shapes andarrangements affect their reality. The cosmetics industry must pay attention to ways of affectingconsistency and texture. Plants produce starches. Animals such as ourselves produceglycogen.This is similar in principle to amylopectin, but is more highly branched, about every 12 glucosesubunits. There is one final variation on polysaccharide formulae based solely on glucose units.When we converted our open chain formula into the ring form, we bent it one way. It could alsohave bent the other way, as shown in figure 8.

Figure 8. Alternative ring structures for glucose

Chains of glucose units formed from 1-4 bonds between molecules of betaglucose are the basisof cellulose. The practical implications will be dealt with later.


11 BIO CHEMISTRY

about25 units

6 CH2OH

O

4

3

2

1

5

3C C 2

C 1

OH5C

C 4

H

O

6 CH2OH

1 1

5

1

2

3

4

6 CH2OH

O

3C C 2

C 1

OH5C

C 4

O

H

6 CH2OH

-glucose -glucose

OH

OH


12/66

1.6 More complex polysaccharidesThe examples we have met so far are based solely on glucose units, combined in various ways.Yet, we managed to produce four distinct substances. Think of the range of possibilities if wecould use two, three, or even more types of subunits in the same polysaccharide. This gives riseto a wide range of complex carbohydrates, such as thepectins and hemicelluloses. Incombination with other bio chemical materials we obtain theglycoproteins, mucopolysaccharidesand so on. Some of these will be mentioned under Uses of carbohydrates (see below) but the

full range is outside the scope of this unit.

1.7 Uses of carbohydratesi) Energy supplyGlucose is the basis of biological energy. It is produced by plants by the process ofphotosynthesis, as summarised below.

Plants then convert the glucose to starch for storage. At some future time, when the plant needsa supply of energy for respiration, it must break down the starch again to give free glucose. Butwhy doesnt it simply store the glucose to begin with?

In my experience, most people give an immediate answer based on the glucose somehowleaking out of the cell. In fact, there are problems getting sugars through cell membranes,which are made of fatty materials. Think back to your experiment with the egg and the sugarsolution. The naked cell membrane was surrounded by a concentrated solution of sugar. Themolecules of sugar could not pass through the fatty membrane, so we had osmosis. In thepresent case, the cells of the plant would attempt to build up a concentrated solution (ofglucose), surrounded by a cell membrane. Water would be drawn in by osmosis. The cells wouldswell. By combining the glucose molecules and storing granules of starch, which are, to allpractical purposes, insoluble in these conditions the cells avoid this difficulty. Similarly, we useglucose as a simple, soluble means of transporting carbohydrate. We store insolublepolysaccharide (glycogen).

ii) StructuralCellulose is probably the most widespread bio chemical molecule, strengthening the cell walls ofplants and bacteria. We have seen that its beta 1-4 bonds are a different shape from alpha 1-4bonds, such as in starch. (No animal can make an enzyme which can break down such bonds.We have amylases, which break down alpha 1-4 bonds, for example, in saliva. We cannotdigest beta l-4 bonds. Animals which eat exclusively plant-based foods rely on specially modifiedguts which harbour micro-organisms, for example in the pouches on the stomachs of cows or inthe appendix of rabbits. These microbes can produce cellulase enzymes.) Have another look atyour glucose model and note that the hydroxyl groups stick out. In the chains of cellulosemolecules, these can interact and form hydrogen bonds, which bind the chains together, so thecellulose chains are locked together into rigid filaments, giving support to the plant cell walls

and, incidentally, making it even harder for animals to digest. Cellulose makes up a largeproportion of fibre in the diet.

Hydrogen bonds are weak. However, imagine, that instead of a molecule being made up solely ofglucose subunits, every half dozen or so along the chain we have some other chemical subunit.Where two chains lie close, these can form strong chemical bonds, and so on to form a complexinterlocking three-dimensional network which could be immensely strong. This is the basis ofcomplex structural carbohydrates in both animals and plants. Plants growing more than a coupleof feet in height must develop more woody support; think of the difference between a small anda tall nettle plant. The Californian Redwood tree can grow to over 200 feet. Ebony is harder thanmild steel. The animal equivalent is chitin in the external skeletons of arthropods. This allows theSouth American Goliath Beetle to grow to 9 inches. Any larger than this and the weight of theskeleton becomes overwhelming. In water, which provides support, the Japanese Spider Crab can

reach 12 feet across the legs, all supported by complex interlocking carbohydrates.


12 BIO CHEMISTRY

Carbon dioxide + water + energy (sunlight) = glucose + oxygen

CO2 + H2O + energy = C6H12O6 + O2


13/66

Hydrogen bonds are weak. However, imagine, that instead of a molecule being made up solely ofglucose subunits, every half dozen or so along the chain we have some other chemical subunit.Where two chains lie close, these can form strong chemical bonds, and so on to form a complexinterlocking three-dimensional network which could be immensely strong. This is the basis ofcomplex structural carbohydrates in both animals and plants. Plants growing more than a coupleof feet in height must develop more woody support; think of the difference between a small anda tall nettle plant. The Californian Redwood tree can grow to over 200 feet. Ebony is harder than

mild steel. The animal equivalent is chitin in the externa skeletons of arthropods. This allows theSouth American Goliath Beetle to grow to 9 inches. Any larger than this and the weight of theskeleton becomes overwhelming. In water, which provides support, the Japanese Spider Crab canreach 12 feet across the legs, all supported by complex interlocking carbohydrates.

Complex, interlocking carbohydrates also have a human structural role, for example in the three-dimensional, water-trapping meshworks (below) which form the matrix or ground substance ofconnective tissues. An example sometimes used as a component in cosmetics is hyaluronic acidinthe dermis of the skin.

We have seen that chains made up from simple sub-units can interact with each other, to formcomplex, three-dimensional structures. If the basic chains also include different sub-groups, whichcan form strong chemical bonds with each other, then these three-dimensional structures can bevery strong, providing support for living organisms.

iii) Water trappingEven starch, a comparatively simple polysaccharide, can trap water to form pastes, as in makingcustard or white sauce. This brings together many of the points we have been exploring about day-to-day properties of materials being dependent on their shapes and interrelationships. In heatingand stirring, the flour is broken up, and starch chains spread through the liquid. As it cools, thechains form hydrogen bonds in a three-dimensional network. This traps the liquid into a gel.

Once again, more complex molecules can extend these possibilities. Imagine a towel. Think of thedifference between a towel made from a smooth fibre and one made from a fluffy fibre. Thelatter soaks up more water. Extend this image to separate molecules. Starch is largely simple

chains. A more highly branched molecule (fluffy) can trap more water. An example is the dermisof the skin which has a matrix containing complex polysaccharides, such as hyaluronic acid.Retention of this water is important for the integrity of the skin. It reduces with age. Glycogen, inthe liver, has large amounts of associated water. It is loss of this, long before any significant loss offat, which accounts for impressive weight losses in the first week of slimming diets. Examples ofeven more impressive water-trapping properties include extracts from seaweeds (agar-agar is wellknown in microbiological plates and alginates are used both in the food and cosmetics industries)and mosses (carrageenates). The record achievement, in terms of water trapping, is probably fromthe latter, 1 gram of which can lock 11 litres of water into a gel.

1.8 SummaryCarbohydrates are a widespread group of substances which can be used to illustrate a number of

basic principles of bio chemical organisation. They can be divided into two broad classes.Comparatively small molecules (sugars) show that a range of substances can be produced bydifferent arrangements of similar chemical units. These can, in turn, be combined into large,complex molecules (polysaccharides). The properties of these depend to a large extent on simpleprinciples of physical shape and interaction. Important bio chemical functions of carbohydrateswhich emerge from these properties include energy supply and storage, structural support andwater retention.


13 BIO CHEMISTRY


14/66

CHECKLISTAt the end of this section you should be able to: draw a structure for a simple carbohydrate such as glucose

use molecular models to distinguish between isomers of carbohydrates, such as aldoses andketoses

describe and illustrate how, through the process of condensation, molecules of simple sugarscan combine to form more complex molecules

describe and illustrate how, by extension of the same principles, a variety of large, complexmolecules of polysaccharide can be produced

explain how the properties of these substances, in realistic day-to-day practice, are based ontheir shapes and interconnections, with reference to energy supply, energy storage, watertrapping and rigid, structural molecules.


14 BIO CHEMISTRY


15/66

2 LIPIDS

2.1 IntroductionLipids are not so clear cut as a category of molecules as carbohydrates. They include the oily,greasy and waxy substances which are part of living processes. The cosmetics industry handlesmany such materials: some of these are biological lipids, some others are synthetic alternatives.

Once again, as with many organic molecules, they consist of carbon, hydrogen and oxygen, butthere are no clear proportions of these, as there are with carbohydrates. However, in general,there is much less oxygen in the molecules. The implications of this will be discussed later.Molecules of lipid contain high proportions of hydrogen and carbon. This means that, like themineral hydrocarbons, they are relatively non-polar/hydrophobic; that is they will not mix wellwith water. In contrast, they will dissolve in organic solvents such as ether and chloroform. Thereare four main classes of lipids which are important in the context of the cosmetics industry: fatsand oils; waxes; phospholipids andsteroids.

As with carbohydrates, I will consider the nature of the first in some detail to establish basicprinciples. These can then be applied to the other classes.

2.2 Biological fats and oilsThese are technically called triacylglycerols. They were traditionally known as triglycerides orneutral lipids. They are the fats and oils found in biology and must be distinguished from themineral oils. Other units, in particular, Unit 7 Oils, Fats and Waxes, will make this distinctionapparent and apply the principles explored here to their applications in cosmetic products.

Triacylglycerols are, chemically, esters between glycerol and long chain fatty acids. You willremember that an ester is a compound between an alcohol and a carboxylic acid. (If you areuncertain about any of these points, you should go back to Unit 1 Basic Chemistry.) We metglycerol (in everyday language, glycerine,) in the previous section when developing ourunderstanding of the nature of simple carbohydrates. It has three carbon atoms, each carrying ahydroxyl (alcohol) group, as shown below in figure 9.

Figure 9 The structure of glycerol

There are 3 hydroxyl groups. It can therefore combine with three acid groups (hence,tri-acylglycerols).

2.3 The nature of fatty acids

From your knowledge of basic organic chemistry, you will remember that the simplesthomologous series was the hydrocarbons. These are basically inert, unreactive molecules. Fattyacids are composed of hydrocarbon chains with carboxylic acid end groups. They remaindominated by their long hydrocarbon chains and retain large amounts of such inertness. Theirpredominant features are that they are highly reduced (consisting of little but carbon andhydrogen) and non-polar. As with the mineral hydrocarbons, molecules of long chain fatty acidscan contain the theoretical maximum number of hydrogen atoms (saturated) or can have doublebonds between some pairs of carbon atoms, reducing the number of hydrogen atoms(unsaturated). A few fatty acids are much more common than others in bio chemical fats. Mostof these are also familiar in cosmetic products. Some examples are listed in table 1.


15 BIO CHEMISTRY

H2 C

C

C

OH

OH

OH

H

H2


16/66

Animals such as ourselves cannot produce these poly-unsaturated fatty acids and must obtainthem from their diet. They are therefore known as essential fatty acids. We will discuss thisfurther under Uses. A molecule of triacylglycerol will have a formula something like that shownbelow in figure 10, depending on which fatty acids are involved.

Figure 10. Structure of a triacylglycerol


16 BIO CHEMISTRY

Table 1. Examples of common fatty acids

Name Degree of saturation Molecular composition

Stearic acid Saturated C18.0*

Palmitic acid Saturated C16.0

Oleic acid Unsaturated (monounsaturated) C18.1

Linoleic acid Unsaturated (polyunsaturated) C18.2

Linolenic acid Unsaturated (polyunsaturated) C18.3

Arachidonic acid Unsaturated (polyunsaturated) C20.4

(* the first number denotes the number of carbon atoms in the chain;the second number denotes the number of double bonds in the chain)

O

C

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

O

C

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

CH3

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

C

O

H2C

HC

H2C

O

O

O


17/66

2.4 The implications of unsaturation

ACTIVITY 5 Double bonds in hydrocarbon chains(Allow about 6 minutes)

The presence of double bonds has important effects on the shapes of hydrocarbon chains, which

can be demonstrated using a molecular model.

Use your molecular model kit to construct a length of hydrocarbon chain. Join eight carbonatoms (black) into a chain. Fill the remaining bonds with hydrogen atoms. As you handle yourmodel, you will see that it is long and flexible. (Remember that the hydrocarbon chains in fattyacids are twice this length!)

Remove one hydrogen atom from each of two adjacent carbon atoms, somewhere in themiddle. It is now unsaturated.

Construct a double bond between these two carbon atoms. (This will involve bending the greenbonds from your model kit.)

Handle your model and observe its shape around the double bond.

Detach one end of the double bond and exchange it with the other hydrogen atom on thatcarbon. Handle and observe the difference.

Sketch your two molecular models.

1.

2.


17 BIO CHEMISTRY


18/66

A chain of carbon atoms joined by single bonds (saturated) will be flexible. A double bond addsa point of rigidity. In fact, double bonds can be two different shapes. The snaky, twistinghydrocarbon chain can approach the double bond from one side and the continuation after thebond come out from the other side. This is called trans (across). Alternatively, the continuationcan come out from the same side of the double bond. This is called cis. These are illustrated infigure 11 below and should resemble your sketch.

Figure 11. The shapes of double bonds in hydrocarbon chains

An obvious question is, does this matter? Think about this in terms of the physical shapes of themolecules, the ways in which they can interact and how these underlie the properties of the realsubstance. Think about the difference between trying to store string compared with somethingwith rigid bends, say, wire coat hangers. The string can be packed up tightly. Coat hangers have

a perverse ability to tangle. Bits stick out. Look at figure 12, below.

Figure 12 cis unsaturated hydrocarbon chains preventing close packing

In figure 12 you can see that cis unsaturated fatty acids cannot pack closely together. So, if ourlipid material has a high proportion of fatty acids containing cis double bonds, it will be morefluid or oily. If it has more saturated fatty acids, packed together, it will be denser, a fat. A day-to-day illustration would be the difference between lard and corn oil. Animals, like us, tend toproduce mainly saturated fatty acids, giving rise to solid fats. Plants produce more unsaturatedfatty acids and therefore oils. Most naturally occurring unsaturated fatty acids have cis doublebonds. Food processing produces trans double bonds. The health implications of this arecontroversial. We can manipulate these properties industrially. For example, plant oils can behydrogenated, that is, their double bonds can be made saturated, to give solid margarines. Thesame principles are applied to the lipid materials used in cosmetic products, giving a way tomanipulate consistency and texture.


18 BIO CHEMISTRY

C

C

H

H

C

C

H

H

saturated trans

saturatedcis

saturated


19/66

2.5 Other classes of lipidsThe biological waxes are similar in principle to the triacylglycerols, that is, they are esters ofalcohols with fatty acids. However, they contain alcohols other than glycerol. I must emphasiseagain that, here, we are discussing waxes produced by living things, such as beeswax, which isused in cosmetic products. The term wax is also used to mean, like oil, a range of mineralsubstances, such as candle wax. It is also used to mean a wide variety of synthetic substances.Some of these are not organic (based on carbon), for example, silicone waxes, such as furniture

polish. All these categories are used in cosmetic products.

Thephospholipids are the major lipid components of cell membranes. As the name suggests,they contain phosphate groups, as well as glycerol and fatty acids. The combination of thisphosphate, together with other chemical groups, makes part of the molecule more polar (able tomix with water) than the other categories of lipids. This is illustrated in figure 13.

Figure 13. Structure of a phospholipid

These intermediate properties make them excellent emulsifying agents. The best known group ofphospholipids, the lecithins, are widely used in food processing. Their properties are used by thecosmetics industry in the production of liposomes. The cosmetics industry has a range of othersubstances which can be used to stabilise their oil and water systems. Some of these would not

be palatable. (This topic is further discussed later in the course.) The final class of lipids is thesteroids. A typical structure is shown in figure 14.

Figure 14. Structure of a typical steroid

The basic steroid is cholesterol, illustrated in figure 14. It has a poor image, due to its associationwith heart disease. However, it is an essential bio chemical, produced in the liver, as acomponent of cell membranes and as the basic material for producing the steroid hormones,such as oestrogens and cortisones.


19 BIO CHEMISTRY

O

C

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

CH3

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

C

O

CH2

HC

H2C

O

O

OP

O

O-

OCH2CH2N+CH3

CH3

CH3

polar/hydrophilicwill mix with water

nonpolar/hydrophobicwill not mix with water

CH2

CH2

CH2 CH

CH3

CH3

CH

CH

CH2

CH2

CH

C

CH3

CH3CH2

CH2

CH

CH

CH2

CH

C

C

CH3CH2

CH2

CH

CH2HO


20/66

ACTIVITY 6 Comparison of lipid structures(Allow about 5 minutes)

We have met a variety of classes of substances which fall into the general category of lipids. Acomparison will reinforce the theme of the relationship between structure and properties.Compare and contrast the major classes of lipids: triacylglycerols (figure 10); phospholipids(figure 13) and steroids (figure 14). Think about points such as which class would be more polaror non-polar, would the shapes and sizes of the molecules have any influence? Note yourcomments in the grid below.

The basic similarity is all three structures contain high proportions of carbon and hydrogen. Thishydrocarbon dominates the triacylglycerol, with three long chain fatty acids. These are thereforethe most non-polar and unreactive of the three, as anyone who has tried to wash fats and oilsoff dinner plates can say. The phospholipids have more mixed properties, enabling them to

interact with both oils and water (we shall return to this point under Uses). In the steroids, thehydrocarbons are looped into a series of interlocking rings, giving a more compact molecule. Thiscan pass though cell membranes.


20 BIO CHEMISTRY

Triacylglycerols Phospholipids Steroids

Similarities

Differences

Triacylglycerols Phospholipids Steroids


21/66

2.6 Uses of lipidsEnergy supply and storageFats and oils are a rich supply of energy. They have calorific values of around 38 kJ/g, which ismore than twice that of carbohydrates. Think of the difference between a plate of plainspaghetti (largely starch) and one with a rich sauce. Lipids are insoluble in water and thereforedo not cause any problems with osmosis. They fit the criteria we discussed above forpolysaccharides as good storage molecules. Humans store 3-4 months supply of energy in the

form of lipid, we tend to say fat. It is the main energy supply for the heart and for skeletalmuscle for steady, sustained exercise. In contrast, our stores of glycogen would be exhausted bya marathon, a few days fast or a weeks slimming diet. If people are given free access to foodand little need for physical activity, many store more lipid than is fashionable or the mortalitystatistics suggest is good for them.

Other uses of stored lipidsStored lipids (fat) have other uses than energy supplies. Subcutaneous fat gives mechanicalprotection. Think of the experience of a blow somewhere where the layer of fat under the skin isthin, such as the shin. It also gives thermal insulation. Layers of fat contribute to body shape,particularly in women.

Cell membranesFigure 13 described and illustrated the structure of phospholipids. Activity 12 extended this toconsider their properties. They make good emulsifying agents. A double layer allows thehydrophilic parts of the molecules, such as the phosphate groups, to be attracted to water. Inpractice, this means the inside of the cell and the watery fluids bathing it. The hydrophobic partsof the molecule, mainly the long hydrocarbon chains of the fatty acids, twist into the centre ofthe membrane. This gives a bilayer, the basis of a cell membrane.

WaterproofingEveryday experience shows us that covering things with a layer of grease keeps water out. It canbe equally useful for keeping water in. Most surfaces inside the body have a layer of mucus,which is largely lipid, for waterproofing and lubrication. This is important to anyone interested inCosmetic Science because many products are designed to counteract the natural tendency of the

skin to dry out. A good coat of goosegrease, worn daily, would do much to reduce water lossand challenge the signs of ageing. However, this would be cosmetically unappealing. A morepleasant texture can be produced by mixing the grease with water. Molecules with oppositeproperties at each end, such as phospholipids, can hold these together to form emulsions. Theseare explained elsewhere in the course. Phospholipids are also the main emulsifying agents inbody fluids such as the blood.

Essential fatty acidsAnimals such as ourselves cannot produce the polyunsaturated fatty acids. They are thereforeessential in our diet. Many of their body functions are nutritional and beyond the scope of thisUnit. They are the basis for the production of important regulatory substances, such as theprostaglandins. A problem with polyunsaturated fatty acids, particularly when they are found in

cell membranes, is that they are particularly susceptible to oxidising reactions. These trigger chainreactions, leading to rancidity. Both the food industry and the cosmetics industry control this withthe use of preservatives known as antioxidants or free radical scavengers. Some of these aresynthetic. Some are the substances naturally used by the body for the same purpose, such as thevitamins A, C and E.

HormonesSome lipids, in the form of steroids act as hormones in the body. Examples are oestrogens(female hormones), androgens (male hormones) and cortisones. Steroids, being compact lipidmolecules (Activity 12) can pass through cell membranes and have profound effects on theiractivities. Some other hormones are molecules which are water soluble and must work byattaching to the membrane and influencing what can pass through it. Insulin is a good example,influencing the way in which cells can take up sugars. An effect of steroid hormones of

particular importance to the cosmetics industry is that they affect fluid balance. For example,oestrogens (female hormones) tend to cause water retention. This helps to maintain womensskin. This effect reduces with age. The cosmetics industry is sensibly aware of this.


21 BIO CHEMISTRY


22/66

2.7 SummaryThe lipids are a mixed group of bio chemical substances whose main similarity is that they willnot mix with water. This is due to the presence of a high proportion of hydrocarbon in theirmolecules. Major types of lipid include triacylglycerols (fats and oils), waxes, phospholipids andsteroids. Important biological functions of lipids include energy supply and storage, formation ofcell membranes, waterproofing, as nutritionally essential bio chemical metabolites and as themolecular basis for some important hormones.

CHECKLISTAt the end of this section, you should be able to: describe the nature of lipids as biological molecules containing a high proportion of

hydrocarbon, making them immiscible with water.

describe and illustrate the structure of fats and oils as combinations between glycerol and threemolecules of fatty acids.

explain how the insertion of double bonds into molecules of fatty acids alters their shapes andtherefore their physical and biological properties.

compare and contrast the structures of a range of other lipid material, with reference to waxes,phospholipids and steroids.

explain the biological roles of lipids with reference to energy supply and storage, cellmembranes, waterproofing and hormonal activity.


22 BIO CHEMISTRY


23/66

APPENDIX 1

Answers to Activity 1The eggs have been used as experimental models to show how osmotic gain or loss of watercould affect normal body cells. You should have noted that eggs in the sugar solution shrank butthat those in water swelled up and the membrane might even have burst? Your explanationsshould be:

In the saturated sugar solution, glucose molecules were too large to pass through the cellmembrane. Because there was less space for water in the sugar solution, the extracellularconcentration of water was lower than the intracellular concentration. Water can move fairlyeasily through the egg cell membrane, therefore it diffused outwards down its concentrationgradient and the cell decreased in volume.

The reverse situation of course applied to the egg placed in water here, the intracellularfluids of the egg white and yolk contain proteins and other solutes which are too large toeasily pass through the membrane. They, however, decrease the space available for watermolecules, i.e. the relative concentration of water is lower than in the extracellular solution,therefore water enters and the egg cells swell. At the end of the experiment, you should findthat the egg soaked in the sugar solution has gone quite firm.

This is a result of the excessive loss of water and the protein has become coagulated ordenatured.

IMPORTANT NOTEThe experiment illustrates the importance of maintaining a relatively constant balance of solutes(such as glucose, but also of ions) between intracellular and extracellular fluids (especially theblood). The importance of homeostaticcontrol systems will be reinforced during later discussionsof the physiology of blood, the kidney, etc.

If you dont understand these answers, revise the section in the text explaining osmosis.


23 BIO CHEMISTRY


24/66

Notes


24 BIO CHEMISTRY


25/66

3 PROTEINS

3.1 IntroductionProteins are the third class of biological molecules covered in this unit, and are the moleculeswithin biological systems that do the work required for life. In order to relate the effects thatcosmetics products may have on living systems, we need to understand something of the basicprinciples that govern protein structure and function.

The goal of this section, therefore, is to introduce the principles of protein structure and outlinethe essential variety of functions that proteins perform within living systems. First, I will introduceamino acids, which are the basic building blocks of proteins, and then go on to look at howthese building blocks are incorporated into proteins, and ultimately how they define the three-dimensional structure and function. Some of the principles that you learned in the BasicChemistry unit will come in useful as you learn about proteins.

3.2 Amino acidsGeneral structureAmino acids are the basic building blocks of proteins and all have the same basic structure. Theycontain an amino group, a carboxylic acid group and a side chain group bonded to one carbonatom called the -carbon.

Figure 15. General structure of amino acids

Humans have 20 amino acids which are genetically encoded. Of course, these follow the generalstructure outlined above, and differ from each other in the nature of the side chain group. Wewill look more closely at the different side chains later in this section.

Amino acids are chiral. All of them (with the exception of glycine) have an asymmetric-carbonatom. This means it is bonded to four different groups, i.e., the amino group, the carboxylgroup, the side chain and hydrogen. The -carbon atom is the chiral centre. The four groups canbe arranged in two different ways around the chiral centre: one arrangement is the mirror imageof the other. The two forms cannot be superimposed on one another and so are isomeric. Thetechnical term for these two isomeric forms is enantiomers or optical isomers.

ACTIVITY 7 Optical isomers of amino acids(Allow 5 minutes)

A general structure of an amino acid is shown in figure 16. Draw its mirror image in the spaceprovided.

Figure 16. Structure of an amino acid

If you have any difficulty, you could use the molecular model kit to represent one amino acid andthen try to assemble its mirror image. The answer is in Appendix 1 at the end of this section.


25 BIO CHEMISTRY

amino group

R

CH

H2N COOHcarboxylicacid group

side chaingroup

-carbon

H

COOHH2N

R

mirror image


26/66

The side chain for glycine is hydrogen. You should note that as glycine has two hydrogensattached to the -carbon, it isnt chiral it is achiral. This is because with two of the attachedgroups being the same, you cant produce mirror images that are non-superimposable, the twoforms are called the L and D isomers.

The 20 genetically coded amino acids that occur in proteins are all the same single enantiomerand are given the designation L. The example in figure 17 shows Lalanine and D-alanine.

Figure 17. Structure of L-alanine and D-alanine

Single amino acids in aqueous solution are ionised and can act as acids or bases. At neutral pH,7.0, the pH found within cells and maintained within the body, amino acids exist as a doublychargedzwitterion as shown in figure 18.

Figure 18. Ionisation of amino acids

This is electrically neutral, net charge 0.

Note, however that the net charge on specific amino acids also depends on the nature of theside chain. If the side chain is acidic or basic, that too will be ionised at neutral biological pH.Therefore, amino acids with acidic or basic groups will have a net ioniccharge. Forces betweenionic charges (electrostatic) are very strong, so interaction between charged side chain groupswhen incorporated into proteins is important in the maintenance of protein structure (as we shallsee), and in providing the driving force for catalytic activity in some enzyme sites.

Essential amino acidsWe have said that 20 amino acids are genetically encoded. This means that the machineswithin cells that synthesise proteins have the capacity to uniquely recognise each of these aminoacids and incorporate them specifically into their correct place within a given protein. Only nineof these amino acids are required in the human diet, i.e., our bodies cant make them. They are

said to be essential. The essential amino acids are listed in table 2 later on, and include histidine,leucine and lysine.

The remaining 11 amino acids required in proteins can be derived from the essential amino acidsor synthesised from scratch using ingredients from the metabolic pathways within the cell.

Side chain classificationAmino acids can be broadly classified in terms of the properties of the side chain group. Inparticular, thepolarityof the side chain greatly affects the properties of the amino acid. Thepolarity is the ability to interact with water at biological pH (7.0) and the side chains vary greatlyfrom non-polar, hydrophobic (water hating) to highly polar, hydrophilic (water loving) groups.Polar amino acid side chain groups can further be divided into those which are ionically chargedat biological pH and those which are electrically neutral. Other factors that vary between aminoacids and side chains are size and shape. We will see later how these factors; polarity, size andshape of the side chain groups of amino acids are fundamental to determining the structure andfunction of proteins which are made up of amino acid building blocks.


26 BIO CHEMISTRY

H

COOHH2N

CH3

L-alanine D-alanine

CH3 H

H2N COOH

netcharge= 0

COOHH2N

R

COOH3N

Rnetcharge= 0

pH 7.0

aqueoussolution

+ -


27/66

Table 2. Amino acid classification groups


27 BIO CHEMISTRY

CH2

COOH

CH2

CH2

COOH

CH2

OH

CH

OHH3C

CH2

SH

CHCH2H3C CH3

CH2

CH

CH3H3C

CH

CH3H3C

CH2

CH3

CH2

NH

CH2

OH

CH2CH2 S CH3

CH2

CONH2

CH2

CH2

CONH2

HN

COOH

CH2

H2N COOH

CH2

CH2

NH2CH2CH2

CH2

CH2

CH2 NH

NH2

NH

CH2

N

NH

Lysine (E)

Arginine

Histidine (E)

Aspartic acid(Aspartate)

Glutamicacid

(Glutamate)

Serine

Threonine (E)

Cysteine

Asparagine

Glutamine

Lys

Arg

His

Asp

Glu

Ser

Thr

Cys

Asn

Gln

R

H2N COOHBasic (polar, positively charged*)

General structureof amino acids

Acidic (polar, negatively charged*)

Neutral (polar, non-charged*)

* = at pH 7.0(E) = essential

amino acids

Non-polar

Structure of R Name AbbreviationStructure of R Name Abbreviation

Isoleucine(E)

Leucine (E)

Valine (E)

Phenyl-alanine (E)

Alanine

Tryptophan(E)

Tyrosine

Methionine

Proline

Glycine

Ile

Leu

Val

Phe

Ala

Trp

Tyr

Met

Pro

Gly

Special amino acids


28/66

Mention must be made of the two special cases, proline and glycine. Proline is the onlygenetically coded amino acid where the side chain is cyclised into the amino acid nitrogen toform a ring. The amino group is now a secondary amine as opposed to a primary amine in allthe other amino acids. The cyclic structure of proline means it is somewhat less flexible than theprimary amines when it is incorporated into peptides and proteins. This has importantconsequences for the structure of proteins as we shall see later.

The side chain group of glycine is hydrogen, which makes it the smallest amino acid possible.Because of this it is somewhat more floppy than other amino acids, and like proline, this canalso affect protein structure in an important way.

Another amino acid worth special mention is cysteine, which can exist in proteins in two forms.The amino acid cysteine contains a thiol group (sulphur containing) which can be oxidised incombination with another cysteine molecule to form a disulphide bridge as shown in figure 19.

Figure 19. Formation of a disulphide bridge by oxidation

The resulting bridged amino acid is something called cystine. These disulphide bridges betweencysteines are a very important feature in protein structure.

Despite the huge variation in properties that the genetically coded amino acids can confer onproteins, there are several examples of unusual or modified amino acids that occur in nature.Hydroxyproline is a major constituent of the connective tissue protein collagen, and is formed bythe oxidation of proline. The modified amino acids are usually derived in the same way fromgenetically encoded amino acids.

Amino acids with a D configuration are found in some lower organisms, particularly bacteria, asconstituents of cell walls or antibiotics. The Dconfiguration acts as a defence mechanism becauseit is resistant to metabolic and hydrolytic enzymes.

ACTIVITY 8 Influence of amino acid side chains(Allow 10 minutes)

The amino acid side chains play a fundamental role in determining the properties of an individualamino acid. It is therefore worthwhile recognising the side chains and their likely influence.

Figure 20. Amino acid side chain groups


28 BIO CHEMISTRY

+

S SSH

cysteine cysteine cystine

O2HS

CH2

CH2

CH3

CH3

1 2CH2

CH2

CH2

CH2

NH2

3 CH2COOH

4H CH2

OH

5


29/66

Shown in figure 20 are 5 amino acid side chain groups. Assign these side chain groups to theappropriate classification groups listed below.

1.

2.

3.

4.

5.

Side chain classification groups

A. Non-polar

B. Neutral, polar

C. Basic

D. Acidic

E. Special

The answers are provided in Appendix 2.

3.3 PeptidesMolecules of amino acids can be linked via a condensation reaction to form a polymeric chain ofamino acids called apeptide. When two amino acids are condensed together, this forms what isknown as a dipeptide (see figure 21). We saw the same type of reaction in the formation of

polysaccharides from monosaccharides.

Figure 21. Condensation reaction to form a dipeptide

The condensation takes place in this instance between the amino group of one amino acid

molecule, and the carboxylic acid group of another amino acid molecule. The reaction involvesthe loss of water (hence condensation) and forms an amide bond (see figure 22). In peptides thisamide bond linkage is known specifically as a peptide bond.

Figure 22. Structure of a peptide bond

The peptide bond is planar, i.e., the oxygen, carbon and nitrogen atoms lie in one plane. Once adipeptide has been formed, another amino acid molecule can be condensed with a dipeptide toform a tripeptide.


29 BIO CHEMISTRY

+

H2O

H2N C

O

OH

R1

NH

H

COOH

R2

H2N

O

N

R2

R1

COOH

H

N

O

N

OHR1

R2


30/66

ACTIVITY 9 Formation of a tripeptide(Allow 10 minutes)

Earlier you saw how carbohydrate molecules could combine to form a bigger molecule. Aminoacids can also form larger molecules via the process of condensation. To illustrate, try to drawthe resulting tripeptide if the dipeptide and amino acid shown below join together via acondensation reaction.

The answer is provided in Appendix 2.


30 BIO CHEMISTRY

H2N C

O

OHNH

C

CH3

O

H2N

O

OH

phenylalanine alanineleucine

amino acid dipeptide


31/66

Of course you could add a fourth amino acid via condensation to form a tetrapeptide, and a fifthto form a penta-peptide, and so on. This process can continue to form chains of peptides ofvarying length and order of amino acids. These are known collectively aspolypeptides.Polypeptides of sufficient length may become a protein. However, a protein is not just a longpolypeptide!

Key differences between a polypeptide and a protein

A polypeptide is a single chain of amino acids with varying length as we have seen. It need nothave a defined three-dimensional structure. It also need not have a biological function. A proteinmay however, consist of one or more polypeptide chains.

Proteins are very large polypeptides with greater than 50 amino acid residues. They have adefined three-dimensional structure, and all proteins have a distinct biological function.

When condensed into a peptide chain, the portion of the amino acid that remains aftercondensation, i.e., the side chain, the nitrogen and the carbonyl group is known as the aminoacid residue.

Figure 23. Key features of a polypeptide chain

This term is used quite often to describe the side chain groups within a polypeptide chain.

A polypeptide chain contains two amino acid residues which are only partially condensed oneat each end. These are the terminalresidues. The residue at the end with the free amino group iscalled the N-terminal residue or N-terminus, and the residue at the opposite end that has a freecarboxylic acid group is called the C-terminal residue or C-terminus. The chain of atoms thatcomprises the nitrogen, -carbon, and carbonyl carbon is referred to as the peptide backbone. Inpeptide shorthand, using three-letter codes, the peptide chain is always written starting fromthe N-terminus. Thus the tetra-peptide example in figure 23 would be written Leu-Ala-Ser-Phe.

When condensed into a peptide bond, the nitrogen of the amino group is no longer basic, andthe carboxyl group is no longer acidic. This means that the properties if a peptide are very much

dependent on the collective properties of the side chain groups of the amino acid residues.


31 BIO CHEMISTRY

H2N

HN

NH

HN

OH

COOH

O

O

O

N-terminus

C-terminus

N-terminalresidue(leucine)

alanineresidue

serineresidue

C-terminalresidue

(phenylalanine)

polypeptidebackbone


32/66

3.4 ProteinsAs we mentioned earlier, proteins are the molecules within biological systems that do the workrequired for life. They may need instructions on what to do from genetic material (DNA, seelater). They may need energy to carry out their functions (from metabolism), but only proteinsare capable of the enormous diversity of structure and function required to maintain life. Becauseof this, proteins are difficult to classify. The most useful classification is by their function and eventhis is very broad. Within each functional group, there is a vast variation in protein properties as

is outlined below:

Table 3. Protein properties

A complementary way of classifying proteins is on the basis of their shape.

Globular proteins have their polypeptide chains folded into compact shapes and are nearlyalways soluble in aqueous solution. Examples of globular proteins are enzymes and antibodies.

Fibrous proteins have their polypeptide chains extended on one axis rather than folded, andare usually insoluble in water. They tend to serve a structural role. Typical examples are keratinin hair and collagen in connective tissue.

You may think that a long polypeptide chain consisting of single bonds can arrange its atoms inan infinite number of ways in three-dimensional space. The three-dimensional arrangement ofatoms within a molecule is called the conformation. Proteins do have defined structures,however, which determines their biological activity. Furthermore, proteins can be isolated withoutlosing their biological activity thus implying that the conformation of the polypeptide chainwithin proteins is quite stable. We shall see how proteins achieve this stable conformation byconsidering the levels of protein structure.

3.5 Protein structureWe have distinguished proteins from simple polypeptides and said they have a defined structure.The structure of proteins is complex and has several different levels. Each of these levels ofstructure is built upon the previous one in a hierarchical manner, increasing in complexity andscale at each stage, starting with the order of amino acids in the chain, through to the overallthree-dimensional structure of the molecule.


32 BIO CHEMISTRY

Protein type Example and function

Structural protein Keratin, armour-like protein found in hair, skin and nails

Enzymes These are biological catalysts and carry out the chemical reactionson which life depends. They will be covered separately later.

Contractible proteins Myosin and actin, the proteins responsible for muscle contraction

Transport proteins Haemoglobin, responsible for the transport of oxygen in blood

Regulatory proteins Hormones such as insulin which regulates glucose levels in the

bodyProtective proteins Antibodies which recognise foreign substances in the body and

help to eliminate them

Storage proteins Ovalbumin, the major protein of egg white

Genetic protein Histones which help organise the structure of DNA within the cellnucleus


33/66


34/66

Figure 25. Representation of the -helix of a polypeptide chain

This shows the helical arrangement of -carbons and the stabilisation of the helix by hydrogenbonds. The carbonyl group of each amino acid is bonded to the N-H of the peptide bond of theresidue four ahead of it in the linear sequence, and all of the carbonyl and N-H groups in thepeptide chain or backbone participate in hydrogen bonds.

In some structural proteins, lengths of -helix can entwine around each other in a cable-likestructure called a -helical coiled coil, for example, keratin in hair. Shorter lengths of -helix canoccur as structural elements of globular proteins such as enzymes. We shall see this later.

Breaking and re-forming disulphide bridges in hair keratin is the basis of perming where hair isformed into appropriate curls. A solution of a reducing agent is applied with heat. This serves to

break the disulphide bridges into the thiol groups of cysteine. The damp heat disrupts thehydrogen bonds on the -helices and causes them to uncoil and stretch. After the reducingsolution is rinsed off, an oxidising agent is applied. This reforms the disulphide bridges betweencysteines but not in their original positions. The hair fibres reform the -helices but the newdisulphide bridges constrain the fibre and produce the desired curl.

The second main secondary structural element in proteins is the -pleated sheetor -sheet morecommonly. As in the -helix, the peptide bond participates fully in hydrogen bonding. However,the bonding is between different polypeptide chains, or inter-chain, rather than between thesame polypeptide chain or intra-chain.


34 BIO CHEMISTRY

N

O

H

H

O

H

O

N

C

H

O

C

C

N

H

O

C

C

C

N

C

N

HH

C CN

O

C

C

H

NC

C

O

CC

O

N

H

C

NC

NC

C

H

O

H

N

H

C

CN

C

C

N

C

C

O

O

O

H

O

C


35/66

The major difference between the -helix and -sheet is the conformation of the peptide chainbackbone which is in a fully extendedconformation rather than a helical structure. Thepolypeptide chains in a -sheet can run in the same direction as each other a parallel-sheet, orin an opposite direction antiparallel-sheet (see figure 26).

Figure 26. Parallel and anti-parallel -sheets

This type of structure is found in fibrin, the protein of silk and spiders webs. It is more flexiblethan keratin but cannot be stretched.

As the side chain groups stick out of the plane of the -sheet structure (not shown in thediagram), in general only small amino acid residues are compatible with this type of structure,e.g., alanine or glycine. Shorter elements of -sheet secondary structure can be found in globularproteins along with -helices.

Collagen, the tough, fibrous connective tissue has an extremely high proportion of proline,glycine and hydroxyproline in its structure. As such, -helices and -sheets are not available assecondary structural elements. Another structural type, the collagen helixis found instead and isunique to collagen. The elastic connective tissue protein elastin has yet another type of helicalsecondary structure that is neither an -helix or a collagen helix.

We shall see later how the collagen helices are arranged when we discuss higher levels of

protein structure. We shall also compare this with the structure of elastin.

3.6 Tertiary structureThis is the third level of protein structure and is concerned with the gross three-dimensionalstructure of a polypeptide chain and three-dimensional interrelationship between elements ofsecondary structure within a polypeptide chain.

The shape a particular protein adopts is dependent upon a large number of relatively weakinteractions between amino acid side chain groups. Disruption of these weak forces is relativelyeasy and can be done by heat, changes in pH or by heavy metal ions. The disruption of thethree-dimensional structure of protein is denaturation. An everyday example of this can be seenwhenever we cook an egg.


35 BIO CHEMISTRY

N

C

C

N

C

C

N

C

C

N

C

H

O

H

O

H

O

H

O

C

C

N

C

C

N

C

C

N

C

O

H

O

H

O

H

C

O

N

C

C

N

C

C

N

C

C

N

C

H

O

H

O

H

O

H

O N

O

H

O

H

O

H

O

C

N

C

C

N

C

C

N

C

C

H

A B


36/66

Egg albumin, the protein of an egg white, changes on heating from a thick clear solution ofglobular protein to a congealed mass that cannot be returned to its clear soluble state. It is saidto be irreversiblydenatured. Hair perming as we saw earlier is a rather more controlled exampleof protein denaturation.

When a protein is denatured it loses its biological activity. The defined three-dimensionalstructure is lost and the protein assumes a random coilconformation. Under controlled

conditions some proteins can be denatured reversiblyand returned to its original or native state(see figure 27). This is an important technique in biochemistry for purification and isolation ofproteins from mixes of other proteins. As an example we shall return to the enzymeribonuclease.

Figure 27. Denaturing of ribonuclease and its reversal

Breaking the disulphide bridges in a controlled manner removes the constraints on thepolypeptide chains. Concentrated solutions of urea act as a denaturing agent by disrupting thenon-covalent weak forces that hold the peptide chain in its native conformation. The randomcoil ribonuclease is now a simple polypeptide; it has no enzymatic activity. The activity can berecovered by removal of the denaturing agent by a process called dialysis. This is achieved byplacing the denatured protein solution into a semi-permeable membrane that allows the smallurea molecules to diffuse out but leaves the large peptide chain inside.

Reoxidation of the thiol groups to disulphide bridges reform the native structure and allowscomplete recovery of the full enzymatic activity. This shows that the folded conformation adoptedby ribonuclease in its native state is the most energetically favoured out of many. This is generallytrue in all single polypeptide chain proteins. It also shows that the information required to specifythe threedimensional structure and its function is contained in its amino acid sequence.

Thus when a protein is synthesised from instructions contained in the genetic code in DNA of acell, the link between the genetic code for that protein and its function is contained in its aminoacid sequence. A single change to one amino acid in the sequence of a protein may be enoughto disrupt the structure critically and cause catastrophic losses of protein function. This is howthe damaging effects of genetic mutations manifest themselves.

3.7 Forces involved in maintaining tertiary structureCovalent bondsThese are the strongest of the forces involved. Covalent bonds between side chain groups ofresidues occur less frequently than other, weaker forces. They are not responsible for formingtertiary structure, but are formed after the polypeptide chain has folded and help to stabilise thisinitially formed three-dimensional structure. The most important covalent bonding is thedisulphide bridge.

(Other forms of covalent link are found in structural proteins such as collagen and elastin. Thesewill be discussed later).


36 BIO CHEMISTRY

26

84

40

95

58

110

72

65

Ribonuclease Native State

cysteine disulphide bridges

1. Reduction of disulphate bridges2. Denaturation using 8M urea solution

1. Removal of urea by dialysis

2. Air oxidation of thiol groups

Denatured Random Coilno enzyme activity

SH

SH

SH SH

SH

SH

SH26

84

4095

58

110

72 65

SH


37/66

IonicThis type of link occurs between side chain groups that have permanent electric charges atbiological pH, e.g., arsinine, lysine, glutamine and aspartic acid. (See figure 28) These aresometimes calledsalt bridges.

Figure 28. Ionic linkages

Hydrogen bondingWe have seen how hydrogen bonding between peptide bonds in the polypeptide backbonehelps to maintain secondary structure. Hydrogen bonding between side chain groups of aminoacid residues is very important for the maintenance of tertiary structure. All amino acids withpolar side chain groups are capable of hydrogen bonding with each other. Additionally, thehydrophobic amino acid residues tyrosine and tryptophan have groups that are capable offorming hydrogen bonds. Hydrogen bonds are also formed between polar groups and water. Insoluble proteins it is common to find polar and charged groups facing the exterior of the protein.

Hydrophobic interactions

Hydrophobic side chain groups (e.g., those of phenylalanine, leucine, valine, etc.) tend to bemore stable when closely packed together at the centre of a globular protein than when they areexposed to water on the exterior. This is a small-scale molecular analogy to the immiscibility of oiland water. Protein chains will therefore tend to fold spontaneously so that the hydrophobicresidues are buried in the centre and polar and charged groups face the outside.

Van der Waals forcesAtoms of side chain groups in tightly packed polypeptide chains are nearly all at a minimumdistance apart so they maximise the Van der Waals force between them. The final tertiarystructure adopted by a protein develops by folding of the polypeptide chain. Elements ofsecondary structure; -helix, -sheets etc., develop spontaneously in a chain and organisethemselves relative to each other driven by the weak forces of hydrophobic interactions, Van der

Waals forces and finally hydrogen bonding. The final three-dimensional conformation is lockedby covalent bonds such as disulphide bridges.


37 BIO CHEMISTRY

Arg NH

NH2

NH2

LysNH3 OOC Asp

GluO

O

polypeptidechain

polypeptidechain


38/66

To illustrate the tertiary structure of a protein and its composition of secondary structuralelements, examine the diagram of the enzyme carbonic anhydrase (figure 29). Note the -helicesrepresented by helical ribbons and -sheets represented by flat arrows. Note that the three-dimensional structure precisely positions the three key histidine residues at the active site of theenzyme.

Figure 29. Structure of carbonic anhydrase

3.8 Quaternary structureIf a protein consists of more than one polypeptide chain, quaternary structure is the term used todescribe how the chains are packed together. Each polypeptide chain is called a subunitandeach of the subunits has its own secondary and tertiary levels of organisation. Several forcesstabilising the quaternary structure are the same as those found in tertiary structure i.e.,disulphide bridges and weak intermolecular attractive forces.

Multi subunit proteins are large. Examples include haemoglobin, the oxygen carrying protein ofthe blood (4 subunits; molecular weight 64,500); glutamate dehydrogenase a metabolic enzyme(6 subunits; molecular weight 320,000); and pyruvate dehydrogenase complex, a metabolicenzyme system (72 subunits; molecular weight 4,600,000).

Collagen and elastinWe shall now look at the structure of collagen and elastin. We saw earlier how collagen andelastin have their own specific secondary structural elements as a result of their unique aminoacid compositions.

In collagen, the helices are intertwined into a triple helixand these in turn are bound togetherinto long inextensible rod-like fibres by a unique system of covalent cross-links. (See figure 30.)These covalent bonds are stronger than disulphide bridges and help to provide the high tensilestrength of collagen, e.g., in cartilage.


38 BIO CHEMISTRY

CO2

AcNH

Histidine residue at active site

-helix

-pleatedsheet


39/66

Short section of fibre Collagen Collagen

a collagen fibre molecule triple helix

Figure 30. Diagrammatic representation of the structure of collagen

Elastin has a much looser organisation. The short lengths of polypeptide helix are folded andtwisted and have a system of covalent cross links between polypeptide chains similar to collagen,but it allows elastic deformation of the structure without breaking any of the bonds.(See figure 31.)

Figure 31. Structure of elastin illustrating elastic properties of the protein

This is important in tissues such as the lungs and arteries where strength but elasticity arerequired to cope with expansion and contraction.


39 BIO CHEMISTRY

Elastic fibre

Stretch Relax

Singleelastin

molecule

Cross-link

Elastic fibre


40/66

ACTIVITY 10 Levels of protein structure(Allow 10 minutes)

A major determining feature of protein structure relates to the bonds and forces that maintaintheir three-dimensional structure. Here is an opportunity to confirm your understanding of thisrelationship.

Based on what you have learnt, complete the following table:

The answers are in Appendix 2 at the end of this section.

3.9 SummaryThe structure and function of a protein is determined by the properties of the sidechains of itssub-units, amino acids, which are linked together by peptide bonds which form via acondensation reaction. As more amino acids are joined to the chain, a polypeptide is formed.Proteins are made up of one or more polypeptide chains and have a defined three-dimensionalstructure. They also have a biological function. The structure of proteins is made up of four levels:

primary the order of the amino acids in the polypeptide chain secondary the localised structure of polypeptide chains held in place by hydrogen bonds tertiary the three-dimensional relationship between elements of secondary structure held in

place by various forces quaternary the overall three-dimensional structure formed by more than one polypeptide

chain in a given protein.


40 BIO CHEMISTRY

Level of structure Bonds and/or forces involved

Primary

Secondary

Tertiary

Quaternary


41/66

CHECKLISTAt the end of this section you should be able to: draw the basic structure of an amino acid and name its constituent parts

explain the principle of chirality as it applies to amino acids

define essential amino acids

describe the different classifications of amino acid side chains

draw the reaction scheme for two amino acids (or amino acid residues) condensing to form apeptide bond, and identify the peptide bond

define a protein and the different functions it can perform

describe primary, secondary, tertiary and quaternary structures of proteins, to include: understanding the principal forces involved in holding the various levels of structure in place understanding the structural elements present in each level of structure, e.g., -helices, and

some of their properties

compare the structure of collagen and elastin and relate this to their different functions asconnective tissue.


41 BIO CHEMISTRY


42/66

4 ENZYMES

4.1 IntroductionAs we have seen already, one of the most important functions of proteins is as enzymes: theirstructure and function is vital to our biological processes. The word enzyme comes from theGreek, en in andzyme yeast. This reflects the fact that a lot of the knowledge we have todaywas obtained by studying yeasts and other micro organisms.

Enzymes catalyse chemical reactions, typically speeding them up by 108-10

10fold, but it can be

more! The power to catalyse reactions far exceeds all man-made catalysts. Man has been usingthe properties of enzymes for many centuries to produce such things as alcohol and cheese. Inrecent years, the uses of enzymes have become much more sophisticated with enzymes beingused to produce chemicals for the pharmaceutical industry and as active ingredients in washingpowders to attack protein stains.

4.2 Function of enzymesA major function of enzymes is to act as catalysts. However, a more complete definition would be:

Proteins of biological origin which increase the rate of specific reactions without affecting thefinal position of the reaction equilibrium.

Enzymes catalyse reactions by reducing the amount of energy needed to convert compound Athrough a transition state T of higher energy, to compound B (see figure 32 below).

Figure 32. Reaction pathway of an enzyme catalysed reaction

The enzyme reduces the amount of energy, activation energyneeded to convert A to B, somaking it easier to convert A to B. It also makes it easier for B to be converted to A by the samedegree, so the position of the reaction equilibrium remains the same. Enzymes do this selectively,in fact, enzymes are very specific such that any one enzyme only catalyses one reaction or set ofclosely related reactions.


42 BIO CHEMISTRY

A B

Reaction

Energy

Path of Reaction

B

A

Activation energy ofuncatalysed reaction

Activation energy ofenzyme catalysed reaction

T


43/66

4.3 Enzyme classificationClassification of enzymes became necessary because of their vast number and variety, and alsobecause of inconsistencies in the nomenclature that had developed over the years. A useful ruleof thumb is that most enzymes have names that end in -ase, with the main exceptions beingproteolytic enzymes such as trypsin en

Documents

Module 1 Unit 5 Bio Chemistry