BIOLOGICAL COMPOUNDS

Unit 1.1: Chemical Elements and Biological Compounds

Syllabus Objectives

• Learners should demonstrate and apply their knowledge and understanding of:

  • Key elements present as inorganic ions in living organisms: Mg^{2+}, Fe^{2+}, Ca^{2+}, PO_4^{3-}.

  • Importance of water: polarity, hydrogen bonds, surface tension, solvent, thermal properties, metabolite.

  • Structure, properties, and functions of carbohydrates: monosaccharides (triose, pentose, hexose sugars); disaccharides (sucrose, lactose, maltose); polysaccharides (starch, glycogen, cellulose, chitin).

  • Alpha and beta structural isomerism in glucose and its polymerization into storage and structural carbohydrates (starch, cellulose, and chitin).

  • Chemical and physical properties enabling the use of starch and glycogen for storage, and cellulose and chitin as structural compounds.

Water & Inorganic Ions

Biochemistry Key Terms

• Atom: The smallest unit of ordinary matter with the properties of a chemical element.

• Element: A substance made up of only one type of atom.

• Molecule: Two or more atoms chemically bonded together.

• Compound: Two or more elements chemically bonded together.

• Organic Compound: A compound containing carbon and hydrogen, produced by a living organism.

• Inorganic Compound: A compound not containing carbon and hydrogen, and not produced by living organisms.

• Macronutrient: A nutrient required by a living organism in small amounts (e.g., iron, calcium).

• Micronutrient: A nutrient required by a living organism in very small quantities (e.g., copper, zinc).

Inorganic Ions Introduction

• Inorganic ions are also called electrolytes or minerals.

• Important in: muscle contraction, nervous coordination, maintaining osmotic pressure in cells and blood.

• Inorganic: A molecule or ion with no more than one carbon atom.

• Organic: Molecules with a large proportion of carbon atoms.

• Originally, "organic" meant derived from living organisms, and "inorganic" meant not derived from living organisms.

• Two groups:

  • Micronutrients: needed in minute (trace) concentrations (e.g., copper, zinc).

  • Macronutrients: needed in small concentrations.

Inorganic Ions

Magnesium (Mg^{2+})

• Structure: Not specified in the text.

• Importance in plants:

  • Component of chlorophyll molecules.

  • Deficiency causes chlorosis.

  • Stunted plant growth due to lack of glucose (reduced photosynthesis).

• Importance in animals:

  • Needed for teeth and bones.

Iron (Fe^{2+})

• Structure: Not specified in the text.

• Importance in plants:

  • Needed as a cofactor in chlorophyll synthesis.

  • Deficiency also leads to chlorosis.

• Importance in animals:

  • Component of hemoglobin.

  • Hemoglobin transports oxygen in the blood.

  • Iron deficiency leads to anemia.

Phosphate Ions (PO_4^{3-}$)

• Structure: Not specified in the text.

• Importance in plants:

  • Component of DNA, RNA, and ATP.

  • Component of phospholipids in plasma membranes.

• Importance in animals:

  • Component of DNA, RNA, and ATP.

  • Component of phospholipids in plasma membranes.

Calcium (Ca^{2+})

• Structure: Not specified in the text.

• Importance in plants:

  • Component of the middle lamella of cell walls.

  • Deficiency leads to stunted growth due to poor cell wall development.

• Importance in animals:

  • Component of bones and teeth.

  • Deficiency could lead to rickets.

Question 1: Magnesium Deficiency in Plants

• When plants lack magnesium, their leaves turn yellow because magnesium is a component of chlorophyll. Less chlorophyll is synthesized, and since chlorophyll is a green pigment, the leaves appear yellow due to other (yellow) pigments becoming more visible.

Metabolism

Metabolic Reactions

• All organisms carry out complex chemical reactions.

• Enzymes govern all reactions.

• Metabolic reactions take place inside living cells or organisms.

• Two types:

  • Anabolic reactions: building up molecules.

  • Catabolic reactions: breaking down molecules.

Examples of Anabolic and Catabolic Reactions

• Anabolic Reactions:

  • Protein synthesis

  • Production of starch/glycogen

  • Photosynthesis

• Catabolic Reactions:

  • Digestion of food

  • Decomposition

Polymers and Monomers

• Monomers are small individual molecules that join to form a larger, more complex polymer.

• Living organisms are primarily made up of water, carbohydrates, lipids, proteins, and nucleic acids.

Biological Compounds and Their Monomers/Polymers

Water

Structure of Water

• Water is a medium for metabolic reactions and a vital cell constituent (65-95% of mass).

• Approximately 70% of human mass is water.

• Water (H_2O) consists of two hydrogen atoms covalently bonded to one oxygen atom.

• Shared electrons are not shared equally; oxygen has greater affinity, pulling electrons closer.

• This results in positive and negative charged ends, making it a polar molecule (dipole).

• Charges are small, written as \delta^− and \delta^+.

• A dipole is a molecule with positive and negative ends but no overall charge.

Hydrogen Bonds

• Many water properties result from its ability to form hydrogen bonds.

• The slightly negative oxygen atom attracts the slightly positive hydrogen atom of another water molecule.

• This uneven charge distribution allows hydrogen bonds between a hydrogen atom and the oxygen atom of another water molecule.

• Hydrogen bonds are weak, but numerous, making it difficult to separate water molecules, giving water its range of properties vital for life.

• Hydrogen bonds can occur between a hydrogen atom with a partial positive charge and an atom with a partial negative charge, such as nitrogen.

• Numerous hydrogen bonds make water a very stable structure.

• H^+ and OH^− participate in chemical reactions.

Properties of Water

A. Polar Molecule

• Makes a good solvent (polar substances dissociate forming solutes).

• Good for transport (non-viscous).

• Good reaction medium.

• Adheres to surfaces (to aid transport in xylem).

B. Forces of Cohesion and Adhesion

• Cohesion: Hydrogen bonding creates a force that 'sticks' water molecules together.

• Adhesion: Water molecules show attraction to other polar molecules.

• Advantage to plants: Cohesion allows water to be held in a continuous column in the transpiration stream; adhesion allows water molecules to adhere to xylem vessel walls.

C. Surface Tension

• Water has a high surface tension.

• Cohesion forces are responsible for the high surface tension, forming a 'skin' where water meets air.

• Water has the highest surface tension of any liquid except mercury.

• The surface of water can behave like an elastic sheet due to cohesion.

• Molecules at the surface pull together more strongly, resembling a stretched membrane.

• A habitat can be produced on the surface of the water (e.g., pond skater).

D. Thermal Properties

• i) High Latent Heat of Vaporization

  • A relatively large amount of energy is needed to turn water from liquid to gas (cooling by sweating).

  • While changing state, a substance absorbs/expels heat without a temperature change (latent heat).

  • Water absorbs a large amount of heat energy while changing from water to vapor due to breaking hydrogen bonds.

• ii) High Specific Heat Capacity

  • Water has a very high specific heat capacity (temperature buffer-good for organisms and enzymes).

  • A large amount of energy is needed to raise the temperature of a body of water.

  • Specific heat capacity: the heat needed to raise the temperature of 1kg of water by 1°C.

  • This maintains a relatively stable internal cell temperature.

• Advantage: Water can absorb large amounts of heat energy before its temperature increases significantly, preventing large temperature fluctuations in aquatic environments.

F. Water as a Solvent

• Water is a universal solvent (dissolves a wide variety of solutes).

• Water can form hydrogen bonds with ions (e.g., NaCl).

• The positive end of the water molecule attracts negative ions, and the negative end attracts positive ions.

• Water molecules surround the ions, causing them to dissolve.

• Importance:

  • Allows chemical reactions to take place in solution.

  • Makes transport inside living organisms much easier (e.g., blood in animals, mineral ions in xylem in plants).

G. Density of Water

• Solid water (ice) has a lower density than liquid water; ice floats.

• Water expands as it freezes and has maximum density at 4°C.

• Water molecules approach each other closely, but as water expands when it freezes, its density decreases.

• In aquatic environments, ice forms an insulating layer, preventing the entire water column from freezing.

• Liquid water beneath the ice has a higher temperature than the air above.

• Water reaches maximum density at 4°C, allowing ice to form on top, insulating lakes/ponds and preventing them from freezing completely and killing organisms.

H. Transparency – Transmission of Light

• Water is colorless and transparent to light.

• This is important for plants and algae because sunlight can reach their cells for photosynthesis.

I. Water as a Metabolite

• Water is a reactant in many metabolic reactions (a metabolite).

• Examples:

  • Hydrolysis: water molecules are chemically inserted to break bonds.

  • Photosynthesis: CO2 + H2O \rightarrow Glucose + O_2

• Water can also be a product, e.g., in aerobic respiration (condensation reaction).

J. Buoyancy and Support

• Water supports organisms.

• Examples:

  • Water supports large animals such as whales.

  • Water supports and helps to disperse reproductive structures such as larvae and coconuts.

  • Water helps to maintain the turgidity of plant cells, essential for support in plants.

K. Water as a Transport Medium

• Water remains liquid over a large temperature range and acts as a solvent for many chemicals making it an ideal transport medium.

• Examples:

  • Blood (plasma is mostly water) transports dissolved solutes around the body along with blood cells.

  • Semen (mostly water) carries sperm cells to the fallopian tubes for fertilization.

Carbohydrates

General Information

• Contain the elements C, H, O (chitin also contains N).

• Carbo: carbon molecule; hydrate: combined with water.

• Literally means hydrated carbon.

• General formula: Cn(H2O)_n.

Classification

• Monosaccharides

• Disaccharides

• Polysaccharides

Monosaccharides

• Monomers – single units.

• Classed as sugars due to being sweet, soluble in water, and forming crystals at normal temperatures.

• Further classified according to the number of carbon atoms in their molecules (3-7).

Table of Monosaccharides

| General Formula | n | Type of Carbohydrate | Example | Notes |
| --------------- | - | -------------------- | -------------- | ------------------------------------------ |
| C3H6O3 | 3 | Triose | Glyceraldehyde | An intermediate in respiration | | C5H{10}O5 | 5 | Pentose | Deoxyribose, Ribose | Component of DNA (deoxyribose), RNA and ATP (ribose)|
| C6H{12}O_6 | 6 | Hexose | Glucose, Fructose, Galactose | Glucose- provides energy via respiration, Fructose – Sweetens fruit, Galactose – A milk sugar |

N.B. Do not use the term room temperature.

Glucose

• Monosaccharides can exist as chains or rings.

• Triose sugars are short and exist as straight chains, but pentose and hexose sugars can close up to form more stable ring structures when dissolved in water.

• Glucose is the most abundant monosaccharide with the chemical formula C6H{12}O_6.

• Monosaccharides contain either an aldehyde (-CHO) or a ketone (C=O) group.

Monosaccharide Isomers

Glucose Isomers

• Two isomers of glucose: α-glucose and β-glucose.

• Differences in structural formulae are based on the positions of the OH group and H on carbon 1.

• These different forms result in different biological properties when they form polymers like starch and cellulose.

• Isomers are molecules that have the same chemical formulae but different structural formulae.

Alpha and Beta Glucose Comparison

• In plants and animals, only α-glucose can be broken down in respiration as only enzymes which fit its shape are present.

• α-glucose molecules combine to form starch.

• β-glucose molecules combine to form cellulose.

• α-glucose: the OH group on carbon 1 lies below the plane of the ring.

• β-glucose: the OH group on carbon 1 lies above the plane of the ring.

Functions of Monosaccharides

*(a) As source of energy in respiration - Carbon-hydrogen and carbon-carbon bonds are broken to release energy, which is transferred to make adenosine triphosphate (ATP).
*(b) Building blocks form larger molecules - Glucose for example, is used to make the polysaccharides starch, glycogen and cellulose.
*(c) Intermediates in reactions - e.g. trioses are intermediates in the reactions of respiration and photosynthesis.
*(d) Constituents of nucleotides - e.g. deoxyribose in DNA, ribose in RNA, ATP and ADP.

Disaccharides

• Monosaccharide + Monosaccharide = Disaccharide.

• They all have the chemical formula C{12}H{22}O_{11}.

• They are also classed as sugars because they have the following three properties: o Sweet o Soluble in water o Form crystals at normal temperatures

• In order for two monosaccharides to bond together they undergo a condenstation reaction.

• This involves the elimation of a water molecule.

• A hydroxyl group is lost from one monosaccharide whilst a hydrogen atom is lost from the other.

• The bond that is formed is known as a glycosidic bond.

• The glycosidic bond is named after the carbon atoms that are linked. E.g. in maltose there is a 1,4- glycosidic bond.

Describe the similarities and differences between fructose and galactose (2)

• Similarities – same chemical formula C6H{12}O_6

• Differences – Galactose – 6-sided ring, Fructose 5- sided ring

*Glycosidic bonds are strong covalent bonds.

• Hydrolysis is the chemical insertion of a water molecule in order to break a bond.

Types of Disaccharides:

Testing for Reducing Sugars – The Benedict’s Test

• All monosaccharides and some disaccharides, (like maltose) are reducing sugars.

• Sucrose is not a reducing sugar.

• Receiving an electron is reduction.

• A reducing sugar is a sugar that can donate an electron to (or reduce), another chemical, in this case Benedict’s reagent.

• Benedict’s contains Copper II sulphate and is alkaline.

• Cu^{2+} ions from the copper sulphate are reduced by the –CHO Aldose or C=O Ketone groups in reducing sugars to form Cu^+ ions.

• When heated Benedict’s forms an insoluble brick red precipitate of Copper I oxide.

  • Cu^{2+} + e^- \rightarrow Cu^+

Question and Answers about Testing for Reducing sugars

1. Use the table below:

a. Place the letters in sequence of the increasing concentration of reducing sugar in each sample.

• B, E, A, D, C.
  b. Suggest a way other than comparing colour changes, in which different concentrations of reducing sugar could be estimated. (2)

*Dry the precipitate in each sample and weigh it. The heavier the precipitate the more reducing sugar was present.
c. Explain why it is not possible to distinguish between very concentrated samples, even though their concentrations are different. (1)

• Once all the copper (II)| sulphate has been reduced to copper (I) oxide, further amounts of reducing sugar cannot make a difference.

Test for Non-Reducing Sugars

• Some disaccharides such as sucrose are non-reducing sugars.

• This means they do not change the colour of Benedict’s when heated and so give a negative result.

• To test a non-reducing sugar, it must be broken down into its monosaccharide components by hydrolysis. These monosaccharides can then be tested with Benedict’s as a reducing sugar.

• Benedict’s reagent needs alkaline conditions to work, so alkali is added.

• The non-reducing sugar is first hydrolysed by boiling it with hydrochloric acid so that it will be broken down into its monosaccharides.

• These can then reduce Benedict’s reagent in the normal way.

• So, a non-reducing sugar is identified by a negative reaction to Benedict’s before hydrolysis and a positive result after hydrolysis.
  Result

• A negative result (solution remains blue), after the first reducing sugar test, followed by a positive result, (solution turns red/brown), after the second reducing sugar test, is an indication of a non-reducing sugar.

• Could also test for sucrose by adding the enzyme sucrase. This hydrolyses sucrose into glucose and fructose. The Benedict’s test will then give a positive result. However, enzymes are specific. Sucrase will only hydrolyse sucrose, so other non-reducing sugars will give a negative result.

Quantitative methods

Biosensors

• Biosensors give an accurate measurement of the concentration of sugar present. This is important in monitoring medical conditions such as diabetes, where an accurate measurement of the concentration of blood glucose is required.

Colorimetry

• Prepare a calibration curve by taking a range of known concentrations of a reducing sugar.

• Carry out a Benedict’s test on each one. Then filter the precipitate out of the solution.

• Use a colorimeter to give readings of the amount of light passing through the solutions/light absorbed.

• Plot the reducing sugar concentrations against absorbance or transmission,

• Read values of unknown samples against the calibration curve.

Measuring precipitate

• Filter and dry the precipitate (the residue caught in the filter paper).

• Measure the mass.

• Calibrate known concentrations of glucose.

• Measure the dry mass of the precipitate for the unknown specimen.

• High concentrations give a large quantity of precipitate.

• High quantity of precipitate gives a high value of mass.

• Read against the calibration curve.

*A quantitative test gives a measure of a substance in units, not simply an indication of its presence.

The Polysaccharides

• Polysaccharides are large complex molecules known as POLYMERS.

• Polymerisation is the process of bonding many MONOMERS by condensation reactions to form one large molecule.

• Monomers are the individual monosaccharides which join to form the polysaccharide.

• General formula: (C6H{10}O5)n.

• They are often folded and can also be branched.

• Polysaccharides are not sugars because they are not sweet, not soluble, do not form crystals at normal temperatures.

• Glucose is the main source of energy in a cell and has to be stored. It is soluble in water and so would increase the solute potential of the cell and so would draw water into the cell by osmosis.

• To avoid this glucose is converted into a storage product, a polysaccharide which has no osmotic effect.

• Polysaccharides are large molecules; therefore, they cannot diffuse out of cells.

• They can be highly folded to from compact molecules and so can be stored in a small space.

Two functions:

• Energy/glucose storage

• Structural support

Energy/glucose storage polysaccharides

• These polysaccharides carry a lot of energy in their C-H and C-C bonds.

• Plant cells store glucose as starch.

• Animal cells store glucose as glycogen.

(a) Starch

• Found in plant cells as small grains, especially in seeds and storage organs, like potato tubers.

• It is an energy source in plants and is used by animals as an important component of food, as an energy source.

Structure of Starch

• Starch is a mixture of two polysaccharides bonded together. Both are chains of α-glucose monosaccharides.

• Starch is not found in animals, although animals hydrolyse starch to glucose for respiration.

(i) Amylose

• A long, linear, unbranched chain of α-glucose molecules.

• It is wound tightly into a coiled shape, making the molecule very compact and so a good energy store.

• It is not so good for releasing energy though as it only has two ends for reaction to occur at.

• It has α-1,4-glycosidic bond forming between the 1st carbon atom (C1) on one glucose monomer and the 4th carbon atom (C4) on the adjacent one.

(ii) Amylopectin

• A long-branched chain of α-glucose.

• Its side branches allow the enzymes that break down the molecule to get to the glycosidic bonds easily

• This means glucose can be released quickly, due to there being lots of ends.

• There are α-1,4-glycosidic bonds between the monomers in the main chain and α-1,6-glycosidic bonds between the monomers of the main chain and the side branches.

Characteristics which make starch a good energy store:

• Insoluble, so it does not draw water into or out of a cell by osmosis.

• Compact, so a lot can be stored in a small space.

• When hydrolysed it forms monosaccharides of α-glucose, which is easily transported and used in respiration.

Testing for Starch

• Iodine solution (iodine dissolved in aqueous solution of potassium iodide) reacts with starch.

• The iodine molecules can become trapped within its coils of the amylose chain.

• This causes a colour change from yellow-brown to blue-black.

• This is a qualitative test and an accurate concentration cannot be determined.

• The depth of blue-black colour gives an indication of relative concentration of starch present.

Questions and Answers #2

1. Describe how the structure of starch makes it suited to its function. (6 marks)

*Amylose is a long unbranched chain.
*Which forms a coiled shape.
*This coiled shape is compact and so makes it good for storage.
*Amylopectin is a long-branched chain.
*Its side branches make it good for storage as the enzymes that break it down can reach the glycosidic bonds easily.
*Starch is insoluble in water.
*This means it can be stored in large quantities
*Without the cell being affected by osmosis.

2. Glucose (C6H{12}O6) combines with fructose (C6H{12}O6), to form the disaccharide sucrose. From your knowledge of how disaccharides are formed, work out the formula of sucrose. (1)

• C{12}H{22}O{11} (C6H{12}O6 + C6H{12}O6 - H20)

2. To hydrolyse a disaccharide it can be boiled with hydrochloric acid but if hydrolysis is carried out by an enzyme a much lower temperature (40oC) is used. Why is this? (2)

• Enzymes are denatured at higher temperatures. This prevents them functioning.

(b) Glycogen

• Glycogen is the animal cell equivalent of starch.

• When blood glucose concentration become too high the hormone insulin coverts excess glucose into glycogen.

• Glycogen is a large insoluble molecule that is stored as granules in the liver and muscle cells.

Structure

• Similar structure to amylopectin. It also has both 1,4-glycosidic bonds and 1,6-glycosidic bonds.

• The difference is that glycogen has shorter 1,4- linked chains and more side branches than amylopectin which means that stored glucose can be released quickly.

Structural polysaccharides

• Structural polysaccharides are needed to provide strength and support.

c) Cellulose

• Found in plant cellulose cell walls (fruit and vegetables).

Cellulose chains

• Made up of long chains of β-glucose monomers.

• They can be up to 10 000 glucose units.

• Cellulose is stronger than amylose and is the most abundant polysaccharide found in nature.

• Bond formed = β-1, 4-glycosidic bond, as it forms between carbon atoms 1 and 4 of 2 β-glucose molecules.

• For the β-1, 4-glycosidic bonds to form between the β-glucose molecules alternating glucose molecules must be rotated through 1800. This allows a condensation reaction to occur.

• The position of the -H group and the –OH group on a single carbon are reversed. In the β-glucose the –OH group is above rather than below the ring.

• Results in the –CH2OH group on each β-glucose molecule alternating between being above and below the plane of the ring.

• This results in very long and very straight chains.

• Many cellulose chains (between 60-70) run parallel to each other and form many hydrogen bonds between OH groups of neighboring chains. These bundles of chains are known as microfibrils.

Microfibrils

• Microfibrils are like iron rods in reinforced concrete.

• Many microfibrils form hydrogen bonds with each other to form larger bundles known as macrofibrils.

Macrofibrils

• Macrofibrils have high mechanical strength due to the large number of H-bonds.

• Many macrofibrils form H-bonds with each other to form cellulose fibres.

Cellulose fibres

• The cellulose fibres are not all aligned in the same direction but “crisscross” each other for strength and rigidity.

• Water can move freely through and along the cell wall.

• The strength of the cell wall prevents it from bursting as it would in animal cells.

• The pressure caused by the water makes the cell turgid, supporting the plant through turgor pressure.

Functions of cellulose

• Major component of plant cell walls.

• Provides rigidity to plant cell.

• Prevents cell bursting when water enters by osmosis.

• It exerts an inward pressure that stops any further water entering. As a result, plant cells are rigid, and the cells push against each other.

• Rigid cells are important in stems and leaves. This means that they are turgid for support and in the leaf to maximize surface area for max photosynthesis.

• It allows water and substances dissolved in water to pass freely into and out of cell.

• Microfibrils have special roles in guard cell walls. Here the arrangements of the Microfibrils allow stomata to open and close.
  Digestion of cellulose

• Cellulose cannot be easily hydrolysed by amylase, as the enzyme’s active site does not fit the glycosidic bonds between the β-glucose monomers, like it does the α-glucose monomers of starch and glycogen.

• Herbivores like cows and elephants can digest cellulose as they have micro-organisms in their gut that produce cellulases that digest cellulose.

• Humans cannot do this, but cellulose is important in our diet as a source of fibre.

• This helps peristalsis occur and reduces colon cancer occurrence.

Extension information

Hemicellulose

• Hemicellulose is present in most plant cell walls along with cellulose.

• A hemicellulose is any of several heteropolymers (matrix polysaccharides).

• They are embedded in the cell walls and form a ‘ground’. They bind with pectin and cellulose to form a network of cross-linked fibres.

• Whilst cellulose is strong and resistant to hydrolysis, hemicellulose has an amorphous structure with little strength. It easily hydrolysed by a dilute acid or base as well as hemicellulose enzymes.

• Whilst cellulose is made of repeating units of B-glucose units with no branching, hemicellulose is made of different sugar monomers and is branched.

Lignin (not a carbohydrate)

• In wood cellulose is further strengthened by lignin.

• Lignin is a complex, organic polymer.

• They are one of the main classes of structural materials in the support tissues of vascular plants and some algae.

• Lignins are particularly important in the formation of cell walls, especially in wood and bark, because they lend rigidity and do not rot easily.

• Lignin fills the spaces in the cell wall between cellulose, hemicellulose and pectin. This is particularly true in xylem vessels elements and tracheids.

• Lignin is a waterproof substance so makes cells impermeable to water. It also increases the mechanical strength of the cell.

(d) Chitin

• A structural polysaccharide which is similar in structure to cellulose.

• It is made of β-glucose subunits in which alternating units are rotated through 180o to each other.

• Linked by β-1,4- glycosidic bonds.

• The subunits are called glucosamine.

• Glucosamine units are the same as β -glucose units except that an OH groups (on C2) is replaced by a nitrogen containing acetylamine group (NH.OCCH3).

• The acetylamine group allows even more hydrogen bonds to form between chains than in cellulose making chitin stronger than cellulose.

Properties

• Strong

• Lightweight

• Waterproof

• Due to its properties chitin is found in the exoskeletons of arthropods and the cell walls of some fungi.

(e) Peptidoglycan

• A polysaccharide composed of acetylamine sugars attached to cross-linked short peptides in the cell wall of some bacteria.

• This forms a mesh-like structure which gives structural strength to the bacterial cell wall as well as counteracting changes in osmotic pressure of the cytoplasm.

• Gram positive bacteria have a thicker peptidoglycan cell wall than gram negative bacteria which makes gram positive bacteria more susceptible to certain antibiotics.

• These antibiotics work by inhibiting peptidoglycan formation.

Unit 1.1: Chemical Elements and Biological Compounds

Syllabus Objectives

• Key elements present as inorganic ions in living organisms: Mg^{2+}, Fe^{2+}, Ca^{2+}, PO_4^{3-}.

• Importance of water.

• Structure, properties, and functions of carbohydrates.

• Alpha and beta structural isomerism in glucose and its polymerization into storage and structural carbohydrates.

• Chemical and physical properties enabling the use of starch and glycogen for storage, and cellulose and chitin as structural compounds.

Water & Inorganic Ions

Biochemistry Key Terms

• Atom: The smallest unit of ordinary matter with the properties of a chemical element.

• Element: A substance made up of only one type of atom.

• Molecule: Two or more atoms chemically bonded together.

• Compound: Two or more elements chemically bonded together.

• Organic Compound: A compound containing carbon and hydrogen, produced by a living organism.

• Inorganic Compound: A compound not containing carbon and hydrogen.

• Macronutrient: A nutrient required by a living organism in small amounts.

• Micronutrient: A nutrient required by a living organism in very small quantities.

Inorganic Ions Introduction

• Inorganic ions are also called electrolytes or minerals.

• Important in: muscle contraction, nervous coordination, maintaining osmotic pressure.

• Inorganic: A molecule or ion with no more than one carbon atom.

• Organic: Molecules with a large proportion of carbon atoms.

• Two groups:

  • Micronutrients: needed in trace concentrations.

  • Macronutrients: needed in small concentrations.

Inorganic Ions

Magnesium (Mg^{2+})

• Importance in plants: Component of chlorophyll.

  • Deficiency causes chlorosis.

  • Stunted growth due to reduced photosynthesis.

• Importance in animals: Needed for teeth and bones.

Iron (Fe^{2+})

• Importance in plants: Needed as a cofactor in chlorophyll synthesis.

  • Deficiency leads to chlorosis.

• Importance in animals: Component of hemoglobin.

  • Hemoglobin transports oxygen.

  • Iron deficiency leads to anemia.

Phosphate Ions (PO_4^{3-})

• Importance in plants: Component of DNA, RNA, and ATP. Component of phospholipids.

• Importance in animals: Component of DNA, RNA, and ATP. Component of phospholipids.

Calcium (Ca^{2+})

• Importance in plants: Component of the middle lamella of cell walls.

  • Deficiency leads to stunted growth.

• Importance in animals: Component of bones and teeth.

  • Deficiency could lead to rickets.

Question 1: Magnesium Deficiency in Plants

• When plants lack magnesium, leaves turn yellow because magnesium is a component of chlorophyll. Less chlorophyll is synthesized causing the leaves to appear yellow due to other pigments becoming more visible.

Metabolism

Metabolic Reactions

• Organisms carry out complex chemical reactions.

• Enzymes govern all reactions.

• Metabolic reactions take place inside cells.

• Two types:

  • Anabolic reactions: building up molecules.

  • Catabolic reactions: breaking down molecules.

Examples of Anabolic and Catabolic Reactions

• Anabolic Reactions: Protein synthesis, Production of starch/glycogen, Photosynthesis

• Catabolic Reactions: Digestion of food, Decomposition

Polymers and Monomers

• Monomers join to form a polymer.

• Living organisms are made up of water, carbohydrates, lipids, proteins, and nucleic acids.

Biological Compounds and Their Monomers/Polymers

Water

Structure of Water

• Water is a medium for metabolic reactions and a vital cell constituent (65-95% of mass).

• Approximately 70% of human mass is water.

• Water (H_2O) consists of two hydrogen atoms covalently bonded to one oxygen atom.

• Shared electrons are not shared equally making it a polar molecule (dipole).

• Charges are small, written as \delta^− and \delta^+.

• A dipole is a molecule with positive and negative ends but no overall charge.

Hydrogen Bonds

• Many water properties result from its ability to form hydrogen bonds.

• The slightly negative oxygen atom attracts the slightly positive hydrogen atom of another water molecule.

• Hydrogen bonds are weak, but numerous, making it difficult to separate water molecules.

• H^+ and OH^− participate in chemical reactions.

Properties of Water

A. Polar Molecule

• Makes a good solvent (polar substances dissociate forming solutes).

• Good for transport (non-viscous).

• Good reaction medium.

• Adheres to surfaces (to aid transport in xylem).

B. Forces of Cohesion and Adhesion

• Cohesion: Hydrogen bonding creates a force that 'sticks' water molecules together.

• Adhesion: Water molecules show attraction to other polar molecules.

• Advantage to plants: Cohesion allows water to be held in a continuous column; adhesion allows water molecules to adhere to xylem vessel walls.

C. Surface Tension

• Water has a high surface tension.

• Cohesion forces are responsible for the high surface tension, forming a 'skin'.

• Molecules at the surface pull together more strongly.

• A habitat can be produced on the surface of the water (e.g., pond skater).

D. Thermal Properties

• i) High Latent Heat of Vaporization: A large amount of energy is needed to turn water from liquid to gas (cooling by sweating).

• ii) High Specific Heat Capacity: Water has a very high specific heat capacity (temperature buffer-good for organisms and enzymes).

• Advantage: Water can absorb large amounts of heat energy before its temperature increases significantly.

F. Water as a Solvent

• Water is a universal solvent (dissolves a wide variety of solutes).

• Water can form hydrogen bonds with ions (e.g., NaCl).

• Importance: Allows chemical reactions to take place in solution. Makes transport inside living organisms much easier.

G. Density of Water

• Solid water (ice) has a lower density than liquid water; ice floats.

• Water expands as it freezes and has maximum density at 4°C.

• In aquatic environments, ice forms an insulating layer.

• Water reaches maximum density at 4°C, allowing ice to form on top, insulating lakes/ponds and preventing them from freezing completely.

H. Transparency – Transmission of Light

• Water is colorless and transparent to light.

• This is important for plants and algae because sunlight can reach their cells for photosynthesis.

I. Water as a Metabolite

• Water is a reactant in many metabolic reactions (a metabolite).

• Examples: Hydrolysis, Photosynthesis

• Water can also be a product, e.g., in aerobic respiration (condensation reaction).

J. Buoyancy and Support

• Water supports organisms.

• Examples: Water supports large animals. Water supports and helps to disperse reproductive structures.

• Water helps to maintain the turgidity of plant cells.

K. Water as a Transport Medium

• Water remains liquid over a large temperature range and acts as a solvent for many chemicals making it an ideal transport medium.

• Examples: Blood, Semen

Carbohydrates

General Information

• Contain the elements C, H, O (chitin also contains N).

• Carbo: carbon molecule; hydrate: combined with water.

• General formula: C_n(H_2O)_n.

Classification

• Monosaccharides

• Disaccharides

• Polysaccharides

Monosaccharides

• Monomers – single units.

• Classed as sugars due to being sweet, soluble in water, and forming crystals at normal temperatures.

• Further classified according to the number of carbon atoms in their molecules (3-7).

Table of Monosaccharides

| General Formula | n | Type of Carbohydrate | Example | Notes |
| --------------- | - | -------------------- | -------------- | -------------------------------------------- |
| C_3H_6O_3 | 3 | Triose | Glyceraldehyde | An intermediate in respiration |
| C_5H_{10}O_5 | 5 | Pentose | Deoxyribose, Ribose | Component of DNA (deoxyribose), RNA and ATP (ribose)|
| C_6H_{12}O_6 | 6 | Hexose | Glucose, Fructose, Galactose | Glucose- provides energy, Fructose – Sweetens fruit, Galactose – A milk sugar |

Glucose

• Monosaccharides can exist as chains or rings.

• Glucose is the most abundant monosaccharide with the chemical formula C_6H_{12}O_6.

• Monosaccharides contain either an aldehyde (-CHO) or a ketone (C=O) group.

Monosaccharide Isomers

Glucose Isomers

• Two isomers of glucose: α-glucose and β-glucose.

• Differences in structural formulae are based on the positions of the OH group and H on carbon 1.

• Isomers are molecules that have the same chemical formulae but different structural formulae.

Alpha and Beta Glucose Comparison

• In plants and animals, only α-glucose can be broken down in respiration.

• α-glucose molecules combine to form starch.

• β-glucose molecules combine to form cellulose.

• α-glucose: the OH group on carbon 1 lies below the plane of the ring.

• β-glucose: the OH group on carbon 1 lies above the plane of the ring.

Functions of Monosaccharides

• (a) As source of energy in respiration

• (b) Building blocks form larger molecules

• (c) Intermediates in reactions

• (d) Constituents of nucleotides

Disaccharides

• Monosaccharide + Monosaccharide = Disaccharide.

• They all have the chemical formula C_{12}H_{22}O_{11}.

• In order for two monosaccharides to bond together they undergo a condenstation reaction.

• The bond that is formed is known as a glycosidic bond.

• Glycosidic bonds are strong covalent bonds.

• Hydrolysis is the chemical insertion of a water molecule in order to break a bond.

Types of Disaccharides:

Testing for Reducing Sugars – The Benedict’s Test

• 
  

• All monosaccharides and some disaccharides, are reducing sugars.

• 
  

• Sucrose is not a reducing sugar.

• 
  

• Benedict’s contains Copper II sulphate and is alkaline.

• 
  

• Cu^{2+} ions from the copper sulphate are reduced by the –CHO Aldose or C=O Ketone groups in reducing sugars to form Cu^+ ions.

• 
  

• Cu^{2+} + e^- \rightarrow Cu^+
  

  Concentration of reducing sugar	Colour of solution and precipitate
  None	Blue
  Very low	Green
  Low	Yellowish green
  Medium	Dark brown
  High	Red
  Test for Non-Reducing Sugars

  • Some disaccharides such as sucrose are non-reducing sugars.

  • To test a non-reducing sugar, it must be broken down into its monosaccharide components by hydrolysis.

  • A negative result (solution remains blue), after the first reducing sugar test, followed by a positive result, (solution turns red/brown), after the second reducing sugar test, is an indication of a non-reducing sugar.

  Biosensors

  • Biosensors give an accurate measurement of the concentration of sugar present.

  Colorimetry

  • Prepare a calibration curve by taking a range of known concentrations of a reducing sugar.

  • Carry out a Benedict’s test on each one. Then filter the precipitate out of the solution.

  • Use a colorimeter to give readings of the amount of light passing through the solutions/light absorbed.

  • Plot the reducing sugar concentrations against absorbance or transmission,

  • Read values of unknown samples against the calibration curve.

  Measuring precipitate

  • Filter and dry the precipitate (the residue caught in the filter paper).

  • Measure the mass.

  • Calibrate known concentrations of glucose.

  • Measure the dry mass of the precipitate for the unknown specimen.

  • High concentrations give a large quantity of precipitate.

  • High quantity of precipitate gives a high value of mass.

  • Read against the calibration curve.

  The Polysaccharides

  • Polysaccharides are large complex molecules known as POLYMERS.

  • Polymerisation is the process of bonding many MONOMERS by condensation reactions to form one large molecule.

  • General formula: (C_6H_{10}O_5)_n$$.

  • Polysaccharides are not sugars because they are not sweet, not soluble, do not form crystals at normal temperatures.

  Two functions:

  • Energy/glucose storage

  • Structural support

  Energy/glucose storage polysaccharides

  • These polysaccharides carry a lot of energy in their C-H and C-C bonds.

  • Plant cells store glucose as starch.

  • Animal cells store glucose