AS Biology Biological molecules

OBJECTIVES All should : be able to describe the structure of a water molecule,the H bonds that hold them together & and understand this is responsible for its unusual properties. Be able to describe some of the properties of water and link some to its structure and importance to living organisms Some may: be able to take this a stage further and give detailed explanations of how the H bonds in water control the properties that are so important for living organisms

Unit 2 Module 1 Biological molecules

Unit 2 Module 1 Biological molecules structural proteins transport protein water DNA Proteins enzymes nucleic acids RNA Unit 2 Module 1 Biological molecules phospholipids carbohydrates saccharides lipids triglycerides polysaccharides cholesterol structural storage

The Elements of life 92 naturally occurring elements The atoms of only 16 are commonly found in living organisms 4 account for 99% of the atoms found in living organisms,these are in order of abundance: H hydrogen C carbon O oxygen N nitrogen This is because living organisms are made up of organic molecules Others are calcium(Ca),iron(Fe),potassium(K),sodium(Na), chlorine(Cl),sulphur(S) & magnesium(Mg)

Bonding Atoms are joined together to make molecules and compounds This is done by chemical bonds Most of the molecules making up living organisms have atoms joined by covalent bonds Covalent bonds are shown by lines.They can be single,double or treble.They are formed by sharing electrons Glycine – an amino acid

Covalent bonding Carbon always has 4 covalent bonds with other atoms. Terrestrial life forms are carbon based. This multiple bonding allows carbon to be a framework atom All the biological molecules we will learn about use carbon as a framework atom. Other bonds formed are: Oxygen 2 ,hydrogen 1 & nitrogen 3 ethanol ethene

Covalent bonding

The building blocks of life Living organisms are mainly made up of macromolecules (giant molecules) These are polymers made up of many smaller monomers by a process called polymerisation The main macromolecules are: Polysaccharides Nucleic acids Proteins (polypeptides) Lipids (fats)

The Building Blocks of life MONOMER POLYMER Organic base, sugar & phosphate Amino acids Fatty acids & glycerol monosaccharide nucleotides Nucleic acids polysaccharide lipids proteins

Carbohydrates All contain the elements carbon, hydrogen & oxygen The name comes from hydrated carbon! For every carbon atom there is a water General formula for carbohydrate is Cn(H2O)n Q. Fructose has 6 carbons, what is it formula? What about ribose which is a pentose sugar? There are 2 types of carbohydrate: 1. Simple sugars: Monosaccharide & Disaccharides 2. Polysaccharides

Simple sugars: Monosaccharides Sugars – all end in -ose White,crystalline substances,dissolve easily in water to give sweet solutions. Single sugar molecule – mono = one General formula (C H2O)n where n is the number of carbon atoms So if 6 carbon atoms(a hexose sugar) the molecular formula is C6H12O6 What about pentose sugars(C5) or triose sugars(C3)?

Glucose Most important and widespread monosaccharide. Hexose sugar The 6 carbons are numbered Function:Transported around in the blood and used in cells as a source of energy in respiration. The energy is released in the form of ATP Structural formula 1 2 3 4 5 6 Molecular formula C6H12O6

The ring form of glucose The chain of carbons in hexose(and pentose) sugars is long enough to close up and form a more stable ring structure Carbon atom 1 joins to the oxygen on carbon atom 5

Glucose isomers The new OH formed in the reaction can be above the ring - β glucose or below - α glucose These are isomers-two forms of the same chemical.

Triose,pentose & hexose sugars

Roles of monosaccharides in living organisms A source of energy for respiration. Due to large number of C-H bonds which when broken release a lot of energy This energy is used to make ATP(adenine triphosphate) from ADP(adenine diphosphate) Also used as building blocks to make larger molecules for example: Deoxyribose(pentose) used to make DNA Ribose used to make RNA and ATP Glucose makes up starch,cellulose and glycogen.

Disaccharide formation Two glucose molecules are held close together by an enzyme. Water is lost and a 1-4 glycosidic bond(link) formed . This is a condensation reaction The new molecule is a disaccharide - maltose

A disaccharide - maltose 1-4 glycosidic link

Common Disaccharides

Hydrolysis of maltose – by enzyme maltase

Chemical test for saccharides(sugars) Reducing Sugars Heat the sugar solution with an equal volume of blue benedict's solution for 2-3 minutes at about 90°C A positive result is a brick red precipitate Benedicts solution contains blue Cu2+ ions, the sugar reduces this to the insoluble brick red Cu+ compound Cu2+ Cu+ Electron From sugar

Non reducing sugar test Some sugars are non reducing. They do not reduce benedict's solution One example is sucrose, it must be hydrolysed(broken-down by adding water) to form glucose and fructose This can be done by heating with a few drops of acid at 90°C for a few minutes. Then neutralising the solution with an equal amount of sodium hydroxide solution You will then get a positive result when repeating the benedict's test

lactose fructose glucose sucrose maltose Sugar Type of saccharide? Result of benedicts test for reducing sugar Result of non-reducing sugar test Reducing or non-reducing sugar? lactose fructose glucose sucrose maltose

Quantitative Estimation of glucose concentration in a solution Glucose solution(%) Weight of precipitate (g) Light Transmission of filtrate (%) 0.01 0.05 0.1 0.5 1

Sugars homework a. Glyceraldehyde – C3 Triose Ribose C5 Pentose Glucose & Fructose C6 Hexose b. Glucose is an aldose sugar H-C=O is on C1 c.

d

e alpha glucose OH below the ring beta glucose OH above ring f alpha galactose

Polysaccharide- Structure & Function Polysaccharides are polymers made up of monosaccharide subunits The polymers can be many thousand monosaccharides – making macromolecules Most important are starch,glycogen & cellulose All are polymers of glucose They are insoluble in water and do not taste sweet.

Starch Made up of a mixture of two macromolecules Amylose (20%) and amylopectin (80%)

Amylose Amylose is formed by condensation of a long chain of α glucose using 1α – 4 glycosidic bonds

Amylose α helix The 1α – 4 glycosidic links in amylose mean the glucose monomers are at a slight angle to each other This causes a helix to form This is stabilised by hydrogen bonds

Amylopectin Branching chains of α glucose Branches about once every 25 glucose Branches formed by 1-6 glycosidic bonds The branching structure gives many “ends” to attach new glucose or to remove it. So it is ideal for storing glucose

Starch – Role in living organisms Starch is a store of glucose in plants Plants cannot store sugars as this would increase the osmotic potential (low water potential) of the cells,the solution inside the cells would be too concentrated. This would lead to …. Starch is insoluble and has no osmotic effect

Starch Grains In plants starch is stored as starch grains These are most often found in chloroplasts or in specialised plant structures such as seeds or tubers eg potatoes The helical shape of amylose means it can be packed tightly

Chemical test for Starch Add iodine solution to the material Iodine solution is orange brown A blue black colour is produced on contact with starch This is because the iodine molecules fit into the amylose helix giving the colour

Glycogen Starch is not found in animal cells Glycogen is used to store glucose in animal cells It is very similar to amylopectin but more branched It branches every 8-10 glucoses,again giving plenty of ends to add extra glucose It forms granules which can be seen in muscle & liver cells

Cellulose Cellulose makes up plant cell walls It is a structural polysaccharide It is made up of β glucose where OH is above the ring In order to form a glycosidic bond the other glucose must be upside down. The bond formed is a β1-4 glycosidic bond

Cellulose cross links Cellulose cannot form a helix It exists in long chains Chains lie side by side and hydrogen bonds form between them These form between adjacent glucose molecules and between the chains.

This gives the cellulose molecule great mechanical strength They are insoluble,tough,durable and slightly elastic, ideal structural components 60-70 chains are strongly linked together to form bundles called microfibrils Microfibrils are held together in fibres Fibres make up the plant cell wall

Structure of cellulose

Cellulose fibres are laid down in layers to form the cell wall Fibres are at right angles to increase strength Other molecules help cross linking Older cell walls are reinforced with lignin A glue like matrix(pectins) is laid down in between the fibres to increase strength Similar to reinforced concrete

Cellulose – structure & function High tensile strength of cellulose fibres means they are difficult to break if pulled at both ends Allows the cell to withstand the pressure caused when water enters by osmosis. Gives plant cells strength and rigidity Provides support Despite strength they are freely permeable Even though cellulose contains glucose it cannot be digested by most animals as they do not have the required enzyme cellulase

Other structural polysaccharides Chitin Exoskletons of arthropods Peptidoglycan Cell wall of bacterial cells

Lipids This group contains a wide range of molecules ranging from fats,oils,phospholipids,waxes & steroids They all contain the elements C,H & O Normally much less O The most widespread are TRIGLYCERIDES also known as fats or oils

Triglyceride structure Made up of 3 FATTY ACID molecules And 1 GLYCEROL molecule

Fatty Acid structure Stearic acid an example of a saturated fatty acid. All the carbon atoms in the tail are full,”saturated” with hydrogen Can also be written as CH3(CH2)16COOH

The COOH group is called a CARBOXYLIC ACID group The long “tail” of the molecule is called a HYDROCARBON TAIL This hydrocarbon chain will not dissolve in water it is said to be non-polar or hydrophobic(water hating)

The carboxylic acid group is polar or hydrophilic(water loving)

Unsaturated Fatty Acids These fatty acids contain a double bond It causes a “kink” in the tail These fatty acids melt more easily One double bond is monounsaturated More than one are called polyunsaturated

Glycerol structure Glycerol is a type of alcohol with 3 alcohol groups.

Forming a triglyceride When glycerol combines with a fatty acid it forms a glyceride When it combines with 3 fatty acids it is a triglyceride They combine in a condensation reaction, losing water Forming an ester link

Properties Triglycerides are insoluble in water, they are non-polar molecules The more unsaturated fatty acids the lower the melting point making these oils at room temperature, normally found in plants Animal fats have a higher melting point and are generally solid at room temperature due to saturated fatty acids

Roles of triglycerides ENERGY RESERVES- high number of C-H bonds so much more energy content than carbohydrate-so you need to store less to get the same energy In humans stored around organs and under the skin

Stored in adipose tissue

Under the skin it is also INSULATION eg blubber in sea mammals It can also produce metabolic water when used in respiration by desert animals such as camels Insoluble: so no osmotic effect

Phospholipids In this molecule the glycerol has two fatty acids attached On the 3rd carbon is a phosphate group

Phospholipid examples

Phospholipid properties and roles These molecules have a hydrophobic tail and hydrophilic head They form the membranes of living cells

Cholesterol Not formed from fatty acids and glycerol 4 carbon based rings Small hydrophobic molecule Found between phospholipid tails in membranes Controls membrane fluidity and mechanical strength

Excess cholesterol Many cells make cholesterol from saturated fats Especially liver cells Excess can be deposited in artery walls Causing atherosclerosis

Excess cholesterol is removed in bile It can form gallstones in the gall bladder

Steroid hormones These are made from cholesterol and include:

Chemical test for Lipids Emulsion test Add ethanol to the suspect material and mix well (any fat will dissolve in the alcohol) Filter off the ethanol pour the ethanol into water A milky emulsion will form if fat was present(fat can no longer dissolve and forms small droplets

Proteins(Polypeptides) Proteins make up more than 50% of the dry mass of cells They have many important functions All proteins are made up of amino acids Functions of proteins

active transport channel protein Respiration/ photosynthesis complex intracellular (metabolic) glycoprotein membrane enzymes Extracellular (digestive) Albumin/ globulin blood globular transport antibodies haemoglobin Proteins in living organisms hormones collagen fibrous contractile structural elastin blood Actin/myosin (muscles) Fibrinogen (fibrin) keratin

Proteins in living organisms

Amino Acid Structure NH2 is the a amine or amino group COOH is the carboxylic acid group The R group or amino acid side chain varies. There are 20 different R groups found in nature so giving 20 different naturally occuring amino acids

The 20 naturally occurring amino acids R groups

Amino Acids

The Peptide Bond Amino acids are joined together by a peptide bond Two amino acids joined form a dipeptide

Peptide bond formation

Polypeptide formation Adding more amino acids to the chain forms a polypeptide In cells this occurs in ribosomes A protein molecule may contain many hundred AAs and sometimes more than one polypeptide chain

Protein – Primary structure The sequence of the amino acids in the polypeptide is known as its primary structure A protein of several hundred amino acids has a huge number of possible primary structures A change in one of the AAs can completely alter the properties of the protein

Protein- Secondary Structure This is when parts of the polypeptide chain becomes twisted or folded There are 2 main types of 2° structure:  helix  pleated sheet

Polypeptide α helix                               Proteins form this stable helix due to hydrogen bonding This takes place between –C=O of one A.A And the –N-H of the A.A 4 places ahead

Polypeptide - β Pleated Sheet This looser, straighter shape is also formed by H bonds. This time between –C=O and –N-H of adjacent chains

Proteins may contain both of these secondary structures They are easily disrupted by heat & changes in pH

Biological molecules chemical tests Reducing Sugars Heat the sugar solution with an equal volume of blue benedict's solution for 2-3 minutes at about 90°C A positive result is a brick red precipitate Non reducing sugar (sucrose) Collect some filtrate from the reducing sugar test Add a few drops of acid and heat in a water bath for a few minutes Neutralise with an equal amount of sodium hydroxide solution Repeat the benedicts test, a brick red ppt is a positive result Starch Add orange brown iodine solution to the material A blue black colour is produced on contact with starch Protein Biuret reagent is made by combining equal amounts of Sodium Hydroxide and Copper Sulphate Add biuret reagent to the suspect food or add some dilute sodium hydroxide solution and mix followed by a little dilute copper sulphate solution. The copper ions interact with the amino groups in the protein to give PURPLE colour for a positive result If the solution stays BLUE this is a negative result

Food Testing Starch Add orange brown iodine solution to the material A blue black colour is produced on contact with starch Protein Biuret reagent is made by combining equal amounts of Sodium Hydroxide and Copper Sulphate Add biuret reagent to the suspect food or add some dilute sodium hydroxide solution and mix followed by a little dilute copper sulphate solution. The copper ions interact with the amino groups in the protein to give PURPLE colour for a positive result If the solution stays BLUE this is a negative result