Chapter 12 – Pathways to Biomolecules

Biomolecules

• Biomolecules are molecules such as fats and oils, carbohydrates, proteins and nucleic acids that are found in all living things.

• They have an essential role in the supply of energy to the body, the growth and repair of organs and tissue, the movement of muscles, the activity of nervous and hormonal systems and the elimination of waste.

• Many biomolcules are polymers.

Fats

• Humans can make their own fat internally.• Though this is not usually necessary as fat is

readily available in the food we eat.• Fat is a name used to describe a large number

of organic compounds belonging to an even larger class of biological molecules called lipids.

• Fats and oils are the best known types of lipids.

Fats cont…

• Oil in food have very different structures and properties from hydrocarbon oils.

• Compounds such as waxes and steroids (which include cholesterol) are also lipids.

• Lipids are based mainly on carbon and hydrogen.• They also contain small amounts of oxygen and

sometimes some other elements.• Most lipids are non-polar and insoluble in water.

Fats and Oils• Have very similar chemical structures.• They are simply distinguished on the basis of their physical states at

normal temperatures:– Fats are solids– Oils are liquids

• Most fats and oils are formed by a condensation reaction between a single molecule of glycerol and three molecules of fatty acids.

• Fatty acids contain a carboxyl functional group which reacts with the hydroxyl groups in the glycerol.

• The –COO- groups in fat are ester linkages.• Three molecules of water are also produced in this reaction.• Fats and oils formed from this process are called triglycerides.• Most fats have two or three different fatty acids attached to the

glycerol molecule.• Triglycerides are large, non-polar molecules and therefore are

insoluble in aqueous.

Types of Fats• Fats are distinguishable on the basis of the fatty acids

from which they are made:– Saturated fats are made from fatty acids, such as palmitic

acid, that contain only single carbon-carbon bonds. Saturated fats are generally unreactive and occur as waxy solids at room temperature.

– Monounsaturated fats are made from fatty acids, such as oleic acid, that contain one carbon-carbon double bond.

– Polyunsaturated fats are made from fatty acids, such as linoleic acid, that contain more than one carbon-carbon double bond. Polyunsaturated fats have lower melting temperatures than saturated fats and often occur at liquids, oils, are room temperature. They are more reactive than saturated fats.

Types of Fats cont…

• The different physical states of saturated and polyunsaturated fats are thought to arise because molecules of saturated fats can pack more closely together, resulting in stronger dispersion forces between the molecules.

• The arrangement of the carbon chain sections at the double bond sites of polyunsaturated fats do not permit close packing.

• Consequently saturated fats have higher melting points than unsaturated fats.

What happens to fat in the body?• Chemical digestion of fat does not start until it reaches the small

intestine.• There it is mixed with bile, from the gall bladder.• Bile contains surfactants that convert the fats into an emulsion of

smaller fat globules.• This increases the surface area, meaning it is able to react more

rapidly.• Secretions from the pancreas and the walls of the small intestine

contain enzymes that catalyse the hydrolysis of fat into fatty acids and glycerol; reversing the condensation reaction from which fat was made.

• Enzymes in the small intestine operate best under alkaline conditions.

• Once the fatty acids and glycerol have been absorbed into the body, they are reassembled into triglycerides via condensation reactions. (see page 180).

Condensation and Polymerisation

• The monomers used to make polymers by a condensation polymerisation reaction have a pair of functional groups that are able to react together, producing a new functional groups that links monomers and also produces a small molecule such as water.

• Synthetic polymers such as nylon and polyester are formed in this way, are are proteins, DNA, cellulose and starch.

Carbohydrates

• The main structural component of all plants is a polymer called cellulose.

• Cellulose belongs to a class of compounds called carbohydrates.

• Green plants in the presence of sunlight, convert carbon dioxide and water into a number of substances including the carbohydrate glucose.

• CHOs are a source of energy in our diets.• CHOs are made from the element C, H and O and usually

have the formula Cx(H2O)y, where x and y are whole numbers.

Carbohydrates cont…

• CHOs range in size from small molecules, with Mr’s of between 100 and 200 to very large polymers with Mr greater than 1 million.

Monosaccharides

• Are the smallest CHOs.• The are white crystalline solids that highly

soluble in water. • Most monosaccharides have a sweet taste.• Monsaccharides together with another group of

CHOs called disaccharides are often called sugars.

• The most abundant monosaccharide is glucose.

Monosaccharides cont…

• It has the molecular formula C6H12O6 and the atoms are arranged in a ring.

• Fructose and Galactose have similar structures.• All three of these molecules contain a number

of polar OH groups, enabling them to form hydrogen bonds with water.

• As a results monosaccharides are highly soluble in water.

Glucose

• Is the key energy source in most forms of life.• It is also a major component of the larger

CHOs.• Glucose and its polymer, starch, are more

rapidly digested than other forms of food.

Fructose & Galactose• Are not a abundant as glucose.• Galactose is not found in nature as a free

monosaccharide.• It occurs frequently as a component of larger

CHOs.• Fructose is found in many fruit juices and honey.• Although fructose is a component of other large

biological molecules, its main role in the body is an energy source.

Disaccharides• Is the carbohydrate formed when two monosaccharides

undergo a condensation reaction.• They too dissolve in water, taste sweet and are called

sugars.• Maltose is formed when two glucose molecules react,

with the elimination of a water molecule. (a on next slide)• Notice how the hydroxyl functional groups react to form

the dissacharide and water.• The two rings are joined via an oxygen atom.• This linkage is called a ether (or glycosidic) linkage.

Disaccharides cont…• Lactose and Sucrose are two other disaccharides.• Lactose is made from a condensation reaction of glucose

and galactose.• It is not as sweet as glucose.• Lactose is synthesised in the mammary glands of

mammals and is the main CHO in milk.• Sucrose is formed from a condensation reaction of

glucose and fructose.• It is widely used as a sweetener.• It is found in the sap of trees and the juices of many fruits.

Polysaccharides

• Are polymer carbohydrates made by linking monosaccharides into a chain.

• They are polymers of glucose molecules linked together in different ways by condensation reactions.

• They are generally insoluble in water and have no taste.

• The three most important polysaccharides are: glycogen, starch and cellulose.

Glycogen

• Is found in animals, where it acts as a glucose storage molecule.

• As glucose can be oxidised to produce energ more rapidly than fat, all glucose is polymerised to glycogen to be stored.

• When there is no more storage space for glycogen, the glucose is converted into fat.

• As energy is required, the glycogen is hydrolysed to yield glucose for respiration.

Starch

• The glucose storage molecule in plants; the plants equivalent of glycogen.

• The starch is stored and used at night to meet the plant’s ongoing energy requirements when the glucose production from photosynthesis has ceased.

Digestion• During digestion, the polymers must be broken down to

release the glucose monomers.• The polymers are first hydrolysed.• This hydrolysis is catalysed by enzymes; every 2nd glucose is

hydrolysed to produce maltose.• Another enzyme catalyses the hydrolysis of maltose into

glucose, which absorbed into the body.• These can be regarded as the reverse of condensation

reactions.

Cellulose• The main structural material in plants.• It has a Mr ranging from 50,000 to 2.5 million.• Its chemical structure differs from starch and

glycogen because of the difference the the way the glucose monomers are joined.

A)StarchB)Cellulose

Proteins

• Proteins are found in every cell and are fundamental to cell structure and operation.

• There are thousands of different types of proteins and each

has its own purpose.

Amino Acids

• Proteins are polymers built up from monomer molecules called amino acids.

• Two of the simpler amino acids are glycine and alanine.

• Every amino acid has an amine group and a carboxyl group.

• They have the general formula of H2N-CHZ-COOH

• The major difference between amino acid is the collection of atoms that make up the side chain, known as the Z group.

Amino Acids

Amino Acids cont…

• As a consequence of the polar amino and carboxyl functional groups; amino acids are soluble in water.

• In solution, the amino group can acts as a base, and the carboxyl as an acid.

• As a result, the amino acid molecule in a solution at a particular pH will usually be in the form of +H3N-CHZ-COO-.

• This sort of molecule is called a zwitterion or dipolar ion.

Zwitterion

• A proton has been lost from the acidic carboxyl group and the basic amino group has gained a proton.

• The pH at which an amino acid exists as a zwitterion depends on the structure of the Z group.

• The dual acidic and basic nature of amino acids means that several different forms of an amino acid can be in equilibrium in a solution.

• The predominant form depends on the acidity of the solution.• In acidic solutions, the +H3N-CHZ-COOH form is most

abundant, whereas H2N-CHZ-COO- form is most abundant in alkaline solutions.

Amino Acids cont…

• The ability of amino acids to react with both acids and bases means that they can act as buffers.

• This means they minimise the effect that the addition of H+ or OH- ions to a solution would have on acidity.

Protein Structure

• When a molecule containing a COOH combines with a molecule containing NH2, a condensation reaction occurs to form an amide functional group – CONH2-.

• This links the two molecules.• Water is also formed.

Protein Structure cont…

• Proteins are polymners formed by condensation reactions between amino acids.

• During these reactions the amino acids join and form long unbranched chains.

• The amine group of one amino acid reacts with the carboxyl of another.

• A covalent bond is formed and a molecule of water is eliminated.

Peptides• Molecules made from amino acids are often called peptides.• When two amino acid molecules react together it is called a

dipeptide.• When three molecules react and tripeptide is formed.• A polymer made from amino acids is known as a polypeptide.• Polypeptides built up of more than 50 amino acids are usually

called proteins.• The group of atoms –CONH- that links the amino acids is an

amide group, referred to as a peptide linkage in proteins.

Structure

• The role that any protein fulfils is dependent on its shape.

• This is regarded as being made up of a primary, secondary and tertiary structure.

Primary Structure

• The order of the amino acids is known as the primary structure.

• The entire shape of a protein is a consequence of the order in which the AAs are joined.

Secondary Structure

• Parts of the chain can attract each other creating 3D shapes.

• This coiling, folding or pleating of sections is described as the protein’s secondary structure.

Tertiary Structure• The Z groups in the amino acid units of a protein influence the

overall 3D shape of the molecule.• The Z groups in some amino acids are relatively large and

their size can cause distortions in the protein structure.• Further, some of the side groups are capable of forming

bonds with side groups elsewhere on the protein chain.• As a consequence of such bonds, a variety of protein shapes

exist.• The overall 3D shape adopted by the protein is called its

tertiary structure.

Enzymes

• Many chemical reactions occur more rapidly when a catalyst is present.

• The biological catalysts that accelerate the rate of chemical reactions in living things are a type of protein called enzymes.

• Enzymes control the manufacture of complex substances as well as breaking down the chemicals to provide energy.

Enzymes cont…

• They are usually more efficient than inorganic catalysts, because they allow reactions to occur rapidly within the narrow band of temperature in which life can survive.

• Compared to inorganic catalysts:– Enzymes produce much faster reactions rates: they can increase the rate

of a reaction by as much as 1010 times.– Enzymes operate under milder conditions.– Enzymes are more sensitive: The catalytic activity of many enzymes is

destroyed when they are heated strongly because their delicate structure breaks down. The enzyme is then described as being denatured.

– Enzymes are very selective.

Enzymes cont…

• The catalytic activity of an enzyme depends on its tertiary structure.

• A slight change in its 3D shape can render an enzyme inoperative.

• The active site of an enzyme is usually a flexible hollow or cavity within the molecule.

• Some enzymes have small, non-protein parts called cofactors, such as vitamins or metal atoms associated with the active site.

• These cofactors are necessary for catalytic effect.

The Lock and Key Process

• A reactant molecule, known as the substrate, is manoeuvred into the active site.

• Here, at the surface of the enzyme the reaction takes place.

• The steps are as follows:1. The reactant (substrate) enters the active site.2. Bonds formed between the enzyme and substrate weaken

bonds within the substrate, thus lowering the reaction’s activation energy.

3. The substrate breaks or rearranges into new products and these products are released.

Enzymes cont…• Typically reactions occur at a rate of 1000/second

on an active site.• During respiration the enzyme catalyses the

decomposition of 600000 carbonic acid molecules into carbon dioxide and water each second.

• In many cases the substrate and enzyme bind together because part of the substrate and active site are non polar and so dispersion forces are significant.

Enzymes cont…

• In other cases, the substrate is held in place by the attraction between positive and negative charges, attraction of a metal ion in the enzyme to a negative dipole in the substrate, or hydrogen bonding between enzyme and substrate.

• The selectivity of enzymes is one of their most important features.

• This selectivity arises because the shape and functional groups in the active site of the enzyme allow it to bind only with certain substrates. (Thus the lock and key process).

Lock and Key Bonds

• Some of the bonds that can occur between the substrate and enzyme include:– Ion-dipole interactions– Hydrogen bonds– Ionic interactions– Dispersion forces and dipole-dipole interactions

may also be involved as an enzyme-substrate complex forms.

Denaturation of Enzymes• The bonds responsible for holding the protein chains

in particular shapes are often weak, so slight changes can disrupt the attractions between parts of the chain.

• This causes the chain to unfold and render the protein ineffective.

• A change the destroys the biological ability of a protein is called denaturation.

• It may result due to an increased temperature, a change in pH or the addition of chemicals.

Denaturation of Enzymes cont…

• Enzyme activity is dependent on temperature.• As temperature increases, the rate of reaction

catalysed by the enzyme increases because of increased collisions between enzyme and substrate, until an optimum temperature of 40°C is reached.

• As there is further temperature increase, the protein is denatured and the reaction rate rapidly decreases.

Denaturation of Enzymes cont…

• Enzymes operate effectively within a small pH range.

• Not all enzymes have the same optimum oH.• The ionisation of amino acids is depended on

pH.• The bonds that determine the tertiary structure

of the enzyme are altered as change in pH alter the ionisation of the amino acid residues in the protein.

Denaturation of Enzymes cont…

• Once a protein has been denatured, the unfolded chains tend to form randomly looped structures which come into close contact.

• The chains become entangled and bond with each other, often by disulfide bridges, so that large clumps of protein molecules are formed.

• This process is called coagulation.

Proteins as Markers for Disease

• The body’s natural defences produce proteins called antibodies in the fight against infection caused by bacteria or viruses.

• These antibodies are specific to a particular disease.

• The cells in diseased or damaged body organs may release specific proteins that are unique to that organ.

Proteins as Markers for Disease cont…

• A raised level of these marker proteins in a patient’s blood or tissue can be used to:– Identify a disease at early or advanced stages of

development.– Monitor the progress of the disease.– Measure the effectiveness of treatment.– Test for the recurrence of the disease.

Heart Attack

• A heart attack is caused when the blood supply to a part of the heart muscle is blocked by a clot in one of the cardiac arteries.

• The cardiac cells are starved of oxygen and nutrients and are consequently injured or die.

• The cells in the damaged part of the heart muscle release various cardiac enzymes into the bloodstream.

• Blood levels of these enzymes increase within a few hours after a heart attack and drop back to normal after several days.

Prostate Cancer

• Cancer is an uncontrolled growth of cells.• It is initially diagnosed by digital examination and by

measuring the level of a protein in the blood.• Normally a small amount of this protein is present in

the blood.• Abnormal cancerous or non-cancerous cell growths

block the ducts in the prostate, forcing more of this protein into the bloodstream.

• The concentration of this protein in the blood is used as a marker for possible prostate cancer.