Water

Water is important because it is a major component of cells, typically forming between 70 and 95% of their

mass and it provides an environment for aquatic organisms. It's molecules have an imbalance of charge

(dipolar) and this generates hydrogen bonding between them.

104.5 degrees

Water as a solvent

Water is an excellent solvent for ions and polar molecules (molecules with an uneven charge) because the

water molecules are attracted to them, collect around them and separate them, so that they dissolve. The

chemicals are then free to move around and react with other chemicals and most processes taking place in

living organisms, happen like this in solution. Non-polar molecules like lipids do not dissolve in water and

tend to be pushed together by it. This is important in hydrophobic interactions in protein structure and in

membrane structure. Due to it's ability to dissolve so many molecules, water is an important transport medium

in animals and plants.

Thermal properties

Water molecules are attracted to one another by hydrogen bonds and this restricts the movement of the

molecules. This means that a relatively large amount of energy is required to increase the temperature of water

(it has a high specific heat capacity) and that large bodies of water are slow to change temperature e.g. lakes

and oceans. Due to their high water content, the bodies of organisms are also slow to change temperature and

this makes maintaining a stable body temperature easier.

Water also requires a relatively high amount of energy to become a gas and this can be used as an effective

means of cooling the body by sweating and panting. Conversely, a relatively large amount of energy must be

transferred away from water to make it freeze, which is important for organisms with a high body water

content and for those living in water.

Density and freezing properties

Water is unusual because it's solid form is less dense than it's liquid form. Below 4°c the density of water starts

to decrease and so ice floats on water and insulates the water below it. This reduces the chances of large bodies

of water completely freezing and increases the chances of life in water surviving. These changes in density of

water with temperature are important in the oceans because they set up currents, which circulate nutrients.

High surface tension and cohesion

Water molecules tend to stick together and this is exploited in the way that water moves in long unbroken

columns through the xylem tissue of plants and is an important property in cells. The cohesion of water

molecules generates a surface tension at the surface of water enabling small organisms e.g. pond skaters to

exploit it as a habitat.

Carbohydrates contain 3 elements:

1. Carbon (C)

2. Hydrogen (H)

3. Oxygen (O)

Carbohydrates are found in one of three forms:

1. Monosaccharides

2. Disaccharides (both sugars)

3. Polysaccharides

Monosaccharides

General formula:.

(CH2O)n where n is a number between 3 and 9. They are classified according to the number of

carbon atoms. The monosaccharides you will have to know fall into these categories:

C = 3 = triose

C = 4 = tetrose

C = 5 = pentose

C = 6 = hexose

Trioses: (e.g. glyceraldehydes), intermediates in respiration and photosynthesis.

Tetroses: rare.

Pentoses: (e.g. ribose, ribulose), used in the synthesis of nucleic acids (RNA and DNA), co-enzymes

(NAD, NADP, FAD) and ATP.

Hexoses: (e.g. glucose, fructose), used as a source of energy in respiration and as building blocks

for larger molecules.

All but one carbon atom have an alcohol (OH) group attached. The remaining carbon atom has an

aldehyde or ketone group attached.

Chain form:

Ring form:

Due to the bond angles between the carbon atoms, it is possible for pentoses and hexoses to form

stable ring structures. The carbon atoms are numbered 1 to 5 in pentoses and 1 to 6 in hexoses.

Depending on the orientation of the OH group on carbon 1, the monosaccharide can have either α or

β configurations.

Disaccharides and glycosidic bonds

These are formed when two monosaccharides are condensed together. One monosaccharide loses an

H atom from carbon atom number 1 and the other loses an OH group from carbon 4 to form the

bond.

The reaction, which is called a condensation reaction, involves the loss of water (H2O) and the

formation of an 1,4-glycosidic bond. Depending on the monosaccharides used, this can be an α-1,4-

glycosidic bond or a β-1,4-glycosidic bond.

The reverse of this reaction, the formation of two monosaccharides from one disaccharide, is

called a hydrolysis reaction and requires one water molecule to supply the H and OH to the sugars

formed.

Examples of Disaccharides

Sucrose: glucose + fructose,

Lactose: glucose + galactose,

Maltose: glucose + glucose.

Maltose: glucose + glucose.

Sucrose is used in many plants for transporting food reserves, often from the leaves to other parts

of the plant. Lactose is the sugar found in the milk of mammals and maltose is the first product of

starch digestion and is further broken down to glucose before absorption in the human gut.

Biochemical tests

All monosaccharides and some disaccharides including maltose and lactose are reducing sugars.

These can be tested for, by adding Benedict's reagent to the sugar and heating in a water bath. If

a reducing sugar is present, the solution turns green, then yellow and finally produces a brick red

precipitate. Non-reducing sugars can also be tested for using Benedict's reagent but first require

addition of an acid and heating to hydrolyse (break apart) the sugar. The acid must then be

neutralised using an alkali like sodium hydroxide before carrying out the test as described above.

Polysaccharides

Polysaccharide: Function: Structure: Relationship of

structure to function:

Starch

Main storage

polysaccharide in

plants.

Made of 2 polymers - amylose and

amylopectin.

Amylose: a polymer of glucoses

joined by α-1,4-glycosidic bonds.

Forms a helix with 6 glucose

molecules per turn and about 300 per

helix.

Amylopectin: a polymer of glucoses

joined by α-1,4-glycosidic bonds but

with branches of α-1,6-glycosidic

bonds. This causes the molecule to be

branched rather than helical

Insoluble therefore good

for storage.

Helix is compact.

The branches mean that

the compound can easily

hydrolysed to release the

glucose monomers.

Glycogen

Main storage

polysaccharide in

animals and fungi

Similar to amylopectin but with many

more branches which are also

shorter.

The number and length of

the branches means that

it is extremely compact

and very fast hydrolysis.

Cellulose

Main structural

constituent of

plant cell walls

Adjacent chains of long, unbranched

polymers of glucose joined by β-1,4-

glycosidic bonds hydrogen bond with

each other to form microfibrils.

The microfibrils are

strong and so are

structurally important in

plant cell walls.

Functions of carbohydrates

1. Substrate for respiration (glucose is essential for cardiac tissues).

2. Intermediate in respiration (e.g. glyceraldehydes).

3. Energy stores (e.g. starch, glycogen).

4. Structural (e.g. cellulose, chitin in arthropod exoskeletons and fungal walls).

5. Transport (e.g. sucrose is transported in the phloem of a plant).

6. Recognition of molecules outside a cell (e.g. attached to proteins or lipids on cell surface

membrane).

Biochemical test

Iodine solution or potassium iodide solution can be used to test for the presence of starch. A

positive result changes the solution from an orange-brown to a blue-black colour.

Lipids

Lipids are made up of the elements carbon, hydrogen and oxygen but in different proportions to

carbohydrates. The most common type of lipid is the triglyceride.

Lipids can exist as fats, oils and waxes. Fats and oils are very similar in structure (triglycerides).

At room temperature, fats are solids and oils are liquids. Fats are of animal origin, while oils tend to

be found in plants.

Waxes have a different structure (esters of fatty acids with long chain alcohols) and can be found

in both animals and plants.

Triglycerides

These are made up of 3 fatty acid chains attached to a glycerol molecule.

Fatty acids are chains of carbon atoms, the terminal one having an OOH group attached making a

carboxylic group (COOH). The length of the chain is usually between 14 and 22 carbons long (most

commonly 16-18).

Three of these chains become attached to a glycerol molecule which has 3 OH groups attached to

its 3 carbons. This is called a condensation reaction because 3 water molecules are formed from 3

OH groups from the fatty acids chains and 3 H atoms from the glycerol. The bond between the

fatty acid chain and the glycerol is called an ester linkage.

The 3 fatty acids may be identical or they may have different structures.

In the fatty acid chains the carbon atoms may have single bonds between them making the lipid

saturated. These are usually solid at room temperature and are called fats.

If one or more bonds between the carbon atoms are double bonds, the lipid is unsaturated. These

are usually liquid at room temperature and are called oils.

Functions of lipids

1. Storage - lipids are non-polar and so are insoluble in water.

2. High-energy store - they have a high proportion of H atoms relative to O atoms and so yield more

energy than the same mass of carbohydrate.

3. Production of metabolic water - some water is produced as a final result of respiration.

4. Thermal insulation - fat conducts heat very slowly so having a layer under the skin keeps metabolic

heat in.

5. Electrical insulation - the myelin sheath around axons prevents ion leakage.

6. Waterproofing - waxy cuticles are useful, for example, to prevent excess evaporation from the

surface of a leaf.

7. Hormone production - steroid hormones. Oestrogen requires lipids for its formation, as do other

substances such as plant growth hormones.

8. Buoyancy - as lipids float on water, they can have a role in maintaining buoyancy in organisms.

Phospholipids

A phosphate-base group replaces one fatty acid chain. It makes this part of the molecule (the

head) soluble in water whilst the fatty acid chains remain insoluble in water.

Due to this arrangement, phospholipids form bilayers (the main component of cell and organelle

membranes).

Proteins

Different proteins can appear very different and perform diverse functions (e.g. the water-soluble

antibodies involved in the immune system and the water-insoluble keratin of hair, hooves and

feathers). Despite this, each one is made up of amino acid subunits.

There about 20 different amino acids that all have a similar chemical structure but behave in very

different ways because they have different side groups. Hence, stringing them together in

different combinations produces very different proteins.

Each amino acid has an amino group (NH2) and a carboxylic acid group (COOH). The R group is a

different molecule in different amino acids which can make them neutral, acidic, alkaline, aromatic

(has a ring structure) or sulphur-containing.

When 2 amino acids are joined together (condensation) the amino group from one and the acid

group from another form a bond, producing one molecule of water. The bond formed is called a

peptide bond.

Hydrolysis is the opposite of condensation and is the breaking of a peptide bond using a molecule of

water.

Primary structure of proteins

Due to the bonding and the shape and chemical nature of different amino acids, the shape of a

whole chain of amino acids (a polypeptide or protein) is specific.

This will affect the properties of the protein, just as the type of a necklace depends on the type of

beads and how they are strung together. Therefore, the primary structure depends on the order

and number of amino acids in a particular protein.

For example:Haemoglobin is made up of 4 polypeptide chains, 2α chains and 2β chains, each with a

haem group attached. There are 146 amino acids in each chain. If just one of these is wrong, serious

problems can arise (e.g. sickle cell anaemia). The red blood cells become distorted, the amount of

oxygen they can carry is reduced and blood capillaries can be blocked, leading to acute pains called

crises.

Secondary structure of proteins

This is the basic shape that the chain of amino acids takes on. The 2 most common structures are

the α-helix and the β-pleated sheet.

This has a regular coiled structure like a spring, with the R groups pointing towards the outside of

the helix. Hydrogen (H) bonds are relatively weak but because there are so many, the total binding

effect is strong and stable. The helix is flexible and elastic.

This is composed of 'side by side' chains connected by H bonds. All the peptide linkages are

involved in inter-chain H bonding so the structure is very stable.

Tertiary structure of proteins

This is the overall 3-D structure of the protein.

The shape of the protein is held together by H bonds between some of the R groups (side chains)

and ionic bonds between positively and negatively charged side chains. These are weak interactions,

but together they help give the protein a stable shape. The protein may be reinforced by strong

covalent bonds called disulphide bridges which form between two amino acids with sulphur groups on

their side chains.

These interactions may be electrostatic attractions between charged groups e.g. NH3+ and O- or van

der Waal's forces.

Fibrous proteins are made of long molecules arranged to form fibres (e.g. in keratin). Several

helices may be wound around each other to form very strong fibres. Collagen is another fibrous

protein, which has a greater tensile strength than steel because it consists of three polypeptide

chains coiled round each other in a triple helix. We are largely held together by collagen as it is

found in bones, cartilage, tendons and ligaments.

Globular proteins are made of chains folded into a compact structure. One of the most important

classes are the enzymes. Although these folds are less regular than in a helix, they are highly

specific and a particular protein will always be folded in the same way. If the structure is

disrupted, the protein ceases to function properly and is said to be denatured. An example is

insulin, a hormone produced by the pancreas and involved in blood sugar regulation.

A globular protein based mostly on an α-helix is haemoglobin.

A globular protein based mostly on a β-pleated sheet is the immunoglobulin antibody molecule.

Quaternary structure of proteins

If a protein is made up of several polypeptide chains, the way they are arranged is called the

quaternary structure. Again, each protein formed has a precise and specific shape (e.g.

haemoglobin)

Prosthetic groups

The majority of proteins are assisted in their functions by a prosthetic group. This may a simple

metal ion such as zinc in the enzyme carboxypeptidase, or it may be a complex organic molecule,

such as the haem group in haemoglobin.

Functions of proteins

1. Virtually all enzymes are proteins.

2. Structural: e.g. collagen and elastin in connective tissue, keratin in skin, hair and nails.

3. Contractile proteins: actin and myosin in muscles allow contraction and therefore movement.

4. Hormones: many hormones have a protein structure (e.g. insulin, glucagon, growth hormone).

5. Transport: for example, haemoglobin facilitates the transport of oxygen around the body, a type of

albumin in the blood transports fatty acids.

6. Transport into and out of cells: carrier and channel proteins in the cell membrane regulate

movement across it.

7. Defence: immunoglobulins (antibodies) protect the body against foreign invaders; fibrinogen in the

blood is vital for the clotting process.

Biochemical test:

The reagent used to test for proteins is called biuret reagent. It can be used as two separate

solutions of copper sulphate and potassium or sodium hydroxide or as a ready-made biuret solution.

In either case, a purple colour indicates a positive result.

ENZYMES

The majority of the reactions that occur in living organisms are enzyme-controlled. Without them,

the rate of the reactions would be so slow as to cause serious, if not fatal, damage. Without

enzymes toxins would soon build up and the supply of respiratory substrate would decrease.

Enzymes are proteins and thus have a specific shape. They are therefore specific in the reactions

that they catalyse - one enzyme will react with molecules of one substrate.

The site of the reaction occurs in an area on the surface of the protein called the active site.

Since the active site for all molecules of one enzyme will be made up of the same arrangement of

amino acids, it has a highly specific shape.

Generally, there is only one active site on each enzyme molecule and only one type of substrate

molecule will fit into it.

Chymotrypsin and trypsin both catalyse the hydrolysis of peptide bonds but due to their shapes,

the active site of chymotrypsin only splits bonds after an aromatic amino acid (one containing a ring

of atoms) whereas trypsin only splits bonds after a basic or straight chain amino acid.

This specificity leads to the lock and key hypothesis.

However, it has been discovered that competitors for an active site (similar in shape to the

substrate) could fit even though they are larger than the substrate. This means that the substrate

and active site are a little flexible.

This has lead to the induced fit model...

Induced fit model

When the enzyme and substrate form a complex, structural changes occur so that the active site

fits precisely around the substrate (the substrate induces the active site to change shape).

The reaction will take place and the product, being a different shape to the substrate, moves away

from the active site. The active site then returns to its original shape.

Enzyme controlled reactions

Reactions proceed because the products have less energy than the substrates.

However, most substrates require an input of energy to get the reaction going, (the reaction is not

spontaneous).

The energy required to initiate the reaction is called the activation energy.

When the substrate(s) react, they need to form a complex called the transition state before the

reaction actually occurs. This transition state has a higher energy level than either the substrates

or the product.

Outside the body, high temperatures often supply the energy required for a reaction. This clearly

would be hazardous inside the body though! Fortunately we have enzymes that provide an

alternative way with a different transition state and lower activation energy.

The rate of the reaction without any external means of providing the activation energy continues at

a much faster rate with an appropriate enzyme than without it. The maximum rate that any reaction

can proceed at will depend, among other things, upon the number of enzyme molecules and

therefore the number of active sits available.

Factors affecting the rate of reaction

1. Temperature: enzymes work best at an optimum temperature.

Below this, an increase in temperature provides more kinetic energy to the molecules involved. The

numbers of collisions between enzyme and substrate will increase so the rate will too.

Above the optimum temperature, and the enzymes are denatured. Bonds holding the structure

together will be broken and the active site loses its shape and will no longer work.

2. pH: as with temperature, enzymes have an optimum pH. If the pH changes much from the optimum,

the chemical nature of the amino acids can change.

This may result in a change in the bonds and so the tertiary structure may break down. The active

site will be disrupted and the enzyme will be denatured.

3. Enzyme concentration:at low enzyme concentration there is great competition for the active sites

and the rate of reaction is low. As the enzyme concentration increases, there are more active sites

and the reaction can proceed at a faster rate.

Eventually, increasing the enzyme concentration beyond a certain point has no effect because the

substrate concentration becomes the limiting factor.

4. Substrate concentration: at a low substrate concentration there are many active sites that are not

occupied. This means that the reaction rate is low.

When more substrate molecules are added, more enzyme-substrate complexes can be formed. As

there are more active sites, and the rate of reaction increases.

Eventually, increasing the substrate concentration yet further will have no effect. The active sites

will be saturated so no more enzyme-substrate complexes can be formed.

Cofactors

Most enzymes require additional help from cofactors, of which there are 2 main types:

1. Coenzymes - these are organic compounds, often containing a vitamin molecule as part of their

structure.

Coenzymes are not permanently bound to the enzyme but may be temporarily and loosely bound for

the duration of the reaction and then move away once it is completed. For example NAD, which

transfers hydrogen away from one molecule in a dehydrogenase reaction and takes it to another

molecule (see the Respiration Learn-it).

2. Metal ions - most speed up the formation of the enzyme-substrate complex by altering the charge

in the active site e.g. amylase requires chloride ions, catalase requires iron.

Inhibitors

Inhibitors slow down the rate of a reaction. Sometimes this is a necessary way of making sure that

the reaction does not proceed too fast, at other times, it is undesirable.

Reversible inhibitors:

Competitive reversible inhibitors: these molecules have a similar structure to the actual substrate

and so will bind temporarily with the active site. The rate of reaction will be closer to the maximum

when there is more 'real' substrate, (e.g. arabinose competes with glucose for the active sites on

glucose oxidase enzyme).

Non-competitive reversible inhibitors: these molecules are not necessarily anything like the

substrate in shape. They bind with the enzyme, but not at the active site. This binding does change

the shape of the enzyme though, so the reaction rate decreases.

Irreversible inhibitors:

These molecules bind permanently with the enzyme molecule and so effectively reduce the enzyme

concentration, thus limiting the rate of reaction, for example, cyanide irreversibly inhibits the

enzyme cytochrome oxidase found in the electron transport chain used in respiration. If this cannot

be used, death will occur.

Industrial Enzymes

Industrial uses of enzymes

Many of the reactions catalysed by enzymes have commercial uses. Previously, these reactions were

made to happen without enzymes by using heat and/or strong acids but enzymes offer the following

advantages:

They are specific in their action and are therefore less likely to produce unwanted by-products.

They are biodegradable and so cause less environmental pollution.

They work in mild conditions i.e. low temperatures, neutral pH and normal atmospheric pressure, and

are therefore energy saving.

However, the last advantage can also be seen as a disadvantage as their conditions must be

stringently controlled or the enzyme may become denatured.

To be effective in a production process the enzyme molecule must be brought into maximum contact

with the substrate molecules. The solutions can be mixed in suitable concentrations or

immobilisation of the enzyme may be used. This involves attaching the enzyme to an inert surface

such as plastic beads and then bringing the surface into contact with a solution of the substrate.

Immobilisation has the advantage that the enzyme molecules can be used over and over again, with

the result that a lot of product can be made from a relatively small amount of enzyme. An example

of the use of immobilisation is in the use of lactase. This enzyme hydrolyses lactose (milk sugar),

into glucose and galactose.

Examples of the industrial uses of enzymes

Perhaps the best known use is that of protease in biological washing powders. This enzyme helps to

break down protein stains such as blood at lower washing machine temperatures. This means they

save energy and are gentler on clothes. Some people are allergic to biological washing powders but

this may be overcome by encapsulating the enzymes in wax from which they are only released during

the wash.Another wide spread use of enzymes is that of pectinases in food modification. Pectin is a

substance which, is found in cell walls and helps to hold the structure together. Pectinase is the

name given to a group of enzymes which, break down pectins. They are therefore used to partially

digest fruit and vegetables in baby food and to help extract fruit/vegetable juices.

Inorganic ions

All of the other substances described in this topic are made up of molecules or groups of atoms but

individual atoms in the form of ions are also important to living organisms. Ions are formed when

atoms gain or loose electrons and are therefore positively or negatively charged.

Table showing the role of some important ions in living organisms

Ion Role in living organism

Calcium Ca2+

Calcium phosphate is an important structural component of bones and teeth. Calcium

ions are important in the transmission of nervous impulses and in the contraction of

muscles.

Sodium Na+ Involved in the transmission of nervous impulses and used in the kidney to reabsorb

water and produce concentrated urine.

Potassium K+ Also involved in nervous transmission and contributes to turgidity in guard cells which

control stomatal opening.

Magnesium

Mg2+

Chlorophyll molecules contain magnesium. Some enzymes which catalyse the

breakdown of ATP have these ions at their active sites.

Chloride Cl- Also used in the kidney to produce concentrated urine. Chloride ions help to balance

the positive charge of sodium and potassium ions in cells.

Nitrate

NO3-

Plants use the nitrogen in these ions to make proteins.

Phosphate

PO43-

Used for making nucleotides and with calcium, make calcium phosphate that gives

bones their strength