Section 1: Biological Molecules: Mrs Shuttleworth

What are the 3 types of bonds involved with Biogical Molecules?: 

• Ionic Bonding: ions with opposite charges attract one other. This is a electrostatic attraction. 
• Covalent Bonding: share pairs of electrons in outer shells.
• Hydrogen Bonding: a molecule with an uneven distribution of charge is said to be polarised (polar molecule). 

Monomers and Polymers: 

Monomer: single molecule (mono) e.g. monosaccharide (glucose), amino acids and nucleotides. 

Polymer: long, complex chain of repeating monomers chemically joined together by covalent bonds e.g. polysaccharides (carbohydrate polymers). 

Condenstation and Hydrolysis Reactions: 

• Condensation Reaction: join monomers together to make polymers. Chemical process in whcih two molecules combine to form a more complex one with the elimination of a simple substance; usually water. 
• Hydroysis Reaction: uses water to break down polymers and releases individual monomers. The breaking down of large molecules into smaller ones by the addition of water molecules. 

Monomers and Polymers: 

• Monomer: One of many small molecules that combine to form larger ones such as a polymer
• Polymer: large molecule made up of repeating smaller molecules (monomers) 

Monosaccharides, Disaccharides and Polysaccharides: 

• Monosaccharide: simple sugars e.g. glucose, fructose and galactose.
• Disaccharide: "double sugars" formed from two monosaccarides e.g. maltose, sucrose and lactose 
• Polysaccaride: large molecules formed from many monosaccarides e.g. celluose, starch and glycogen 

Test for Reducing Sugars: 

All monosaccarides and disaccarides are reducing sugars. Reduction is a chemical reaction involving the gain of electrons or hydrogen. 

A Reducing Sugar is therefore a sugar that can dotate electrons to another chemical. 

This test is known as the: BENEDICTS TEST(alkaline solution of copper II sulfate. 

Result: when a reducing sugar is heated with Benedicts reagant it forms a insoluble red precipitate of Copper II oxide. 

Method: 

• Add 2cm3 of food sample 
• Add equal volume of benedicts reagant 
• Heat in gently boiling wtaer for 5 mins 

Dissaccharides:

When combined to pairs, monosaccharides form a dissaccharide for example:

• Glucose +Glucose = Maltose 
• Glucose + Fructose = Sucrose 
• Glucose + Galactose = Lactose 

^Condensation reaction as a molecule of water is removed. The bond formed is called a GLYCOSIDIC BOND. 

Hydroysis:(Breakdown)

When water is added to a disaccharide it breaks the glycosidic bond releasing individual monosaccharides. 

Non-Reducing Sugars Test:

To detect a non-reducing sugar we use the benidicts test. 

In order to detect a non-reducing sugar you first hydroyisis it into its monosaccharide. 

Method:

• Add 2cm3 of food sample to 2cm3 of Benidicts reagent and filter it
• Place in gently boiling wtaer for 5mins 
• If reagent doesn't change colour then a reducing sugar is not present 
• Add another 2cm3 of food to 2cm3 of dilute hydrochloric acid and place in gently boiling water for 5mins 
• The dilute hydrochloric acid will hydroyse any disaccharide 
• Slowly add sodium hydrogencarbonate to neutrilise the hydrochloric acid 
• Test with pH paper to make sure it is alkaline 
• Re-test by heating it with 2cm3 of benidicts in gently boiling water for 5mins

Result: 

If a non-reducing sugar was present in original sample the benidicts will turn orange/brown. 

This is due to the reducing sugars that were produced from the hydroysis of the non-reducing sugar. 

Polysaccharides are polymers formed by combining together many monosaccharides. 

Polysaccharides are long chains of monosaccharides that are joined by glycosidic bonds that were formed by condensation reactions.

• Large molecules= Insoluble: makes them suitable for storage 
• E.g. Celluose= not used for storage but give structural support to plant cells 

Hydroysised: 

When polysaccarides are hydroysied they break down into disaccharides or monosaccharides 

Starch is a polysaccharide that is found in plants in small grains or granules. 

• It is formed by joining lots of alpha glucose molecules by glycodic bonds in series of condensation reactions. 

Test: Change Colour of the Iodine: 

• Place 2cm3 of the sample in test tube 
• Add 2 drops of iodine and shake
• If starch is present it turns the iodine a blue-black colour 

• Polysaccharide 
• Found in seeds and storage organs in plants 
• Major energy source 
• Made up of chains of alpha glucose monosaccharides linked by glycosidic bonds that are formed by condesation reactions 
• Tight coil that makes it very compact 

Role: Energy Storage: 

• Insoluble: doesn't affect water potential: water isn't drawn into cells by osmosis 
• Large + insoluble: doesn't diffuse out of cells 
• Compact: small areas 
• Hydroysis: forms alpha glucose which can be transported for respiration 
• Branched ends: acted on by enzymes, glucose monomers can be released rapidly 

• Short chains 
• Highly branched 
• Major carbohydrate storage 
• Stored in small granules e.g. in muscles and the liver 

Role: Storage: 

• Insoluble: doesn't draw water into cells by osmosis 
• Insoluble:doesn't diffuse out of cells 
• Compact: stored in a small place 
• Highly branched: more ends to be acted on by enzymes, rapidly broken down to form glucose monomers that are used in respiration

• Made of monomers of beta glucose 
• Polysaccharide 
• Straight unbranched chains 
• Unbranched chains run parralel allowing hydrogen bonds to form cross links between chains 
• The sheer overall number of hydrogen bonds makes it stregthen 
• Structural material 
• Grouped= microfibrils 
• E.g. plant= rigidity to plant cell and prevents it from bursting 

Role: Support and Rigidity: 

• Beta glucose molecules and straight unbranched chains 
• Parralel and are cross linked by hydrogen bonds which add collective strength 
• Form microfibrils and add strength 

Characteristics: 

• Contain: carbon, hydrogen and oxygen
• Insoluble in water 
• Soluble in organic solvents such as alcohol 

Main Groups: 

• Triglycerides
• Phospholipids 

Roles of Phospholipids: 

• Source of energy: oxidised can produce lots of energy and release water 
• Waterproofing: insoluble in water, conserves water
• Insulation: fats are slow conductors of heat, retain body heat 
• Protection: stored around organs such as the kidney 

(Fats are solids as room temperature as oils are liquid)

Structure: 

It has 3 fatty acids and one glycerol 

Reactions: 

• Condensation: fatty acid forms an ester bond with glycerol 
• Hydroysis: produces glycerol and 3 fatty acids 

Saturated and Unsaturated: (fatty acids):

• Saturated: no carbon- carbon double bonds 
• Mono-unsaturated: one double bond between carbon atoms 
• Polyunsaturated: more than one double bond between carbon atoms 

Strcuture:

• High ratio of energy storing carbon-hydrogen bonds: good source of energy 
• Low mass to energy ratio: good storage molecules: lots of energy in small stored volume 
• Large + non-polar: insoluble in water: storage does not affect osmosis or water potential 
• High ratio of hydrogen to oxygen atoms: release water when oxidised: good soruce of water

Structure:

1 Fatty acid, 1 glycerol and phosphate 

• Fatty acid: repel water (hydrophobic) 
• Phospahte: attract water (hydrophilic) 

Hydrophobic and Hydrophilic:

• Hydrophobic: away from water 
• Hydrophilic: interacts with water (attracted) 

Polar: position themselves so that the hydropholic heads are close to the water and hydrophobic are far from the water 

Sructure- Properties:

• Polar: form a bilayer within cell surafec membranes: hydrophobic barrier 
• Phosphate heads help to hold the surface of the membrane 
• Phospholipids allows them to form glycolipids by combining with carbohydrates within membrane: cell recognition 

Emulsion Test:

Method:

• 2cm3 of sample, and 5cm3 of ethanol 
• Shake 
• Add 5cm3 of water 
• Shake 
• If there is a cloudly white colour it indicates the lipid 
• Repeat with sample replaced with water 

Results:

• Cloudly colour is due to any lipid in sample to water to form emulsion. Light is refacted as it passes through the oil making it seem cloudly. 

Amino acids are a monomer which combine to make a polymer called a polypeptide. 

Polypeptides can be combined to form proteins. 

Chemical Groups: 

• Amino group (NH2)
• Carboxyl group (-COOH) 
• Hydrogen atom 
• R(side)group= variety of chemical groups 

Drawn: 

Monomer combine to form a dipepeptide etc. 

• Water= it is made by combining an -OH (carboxyl group) with an -H from amino group. 
• Bond = peptide bond (can be broken down by hydroysis to form 2 amino acids 

Drawn General Structure of an Amino Acid: 

Condensation Reactions: series of reactions means many amino acids monomers can be joined= polymerisation (process) 

Chain of many amino acids = polypeptide 

^The sequence of amino acids in the polypeptide forms the primary strcuture of a protein

• The sequence is determined by DNA  
• Primary Structure determines its: shape and function 
• A change in just a single amino acid in the primary sequence can lead to a change in shape of proteins and may stop it working and carrying out its function. 

Linked amino acids that make up a polypeptide processes: 

• NH and -C=O groups on either side of every peptide bond 
• Hydrogen of the -NH group has an overall positive charge while the O of the -C=O group has an overall negeitive charge 
• These 2 groups^ therefore form weak bonds called hydrogen bonds 

This causes the long polypeptide chain to be twisted into a 3D chape, such as the coil known as an alpha helix: (Drawn): 

Definition: alpha helixs of secondary proetin structure can be twisted and folded even more to give a complex and 3D structure of each protein 

Maintained by a number of Bonds: (depend on primary structure) 

• Disulfide bridges
• Ionic Bonds 
• Hydrogen Bonds 

(Compact structure) 

Large proteins containing a number of individual polypeptide chains that are linked differently. 

• Combination of number of different polypeptide chains e.g. haebogoblin

Drawn: 

Biuret test= peptide bonds 

Method: 

• Sample of solution in test tube and add equal volume of sodium hydroxide solution at room temp
• Add few drops of dilute copper (II) sulfate solution 
• Mix 
• A purple coloration indicates the presence of a peptide bond and hence a proetin 
• If no peptide bond is present it will remain blue 

Enzymes are globular proteins that act as catalysts. 

Conditions:

• collide with suffient energy 
• Free energy of the products must be less than that of the substates 
• Require activation energy 

Enzymes work by lowering the activation energy. 

Enzyme Structure:

• They have a specific 3D shape as a result of their sequence of amino acids (primary structure) 
• The active site is made up of a reliatively small number of amino acid s
• Acts on the substrate, when fits it is called a enzyme-substrate complex 

The active forms as the enzyme and substrate interact. 

Substrate- a change in the environment of the enzyme, leads to a change in the enzyme that forms the functional active site- the enzyme is flexible and can mould itself around the substrate (alters in the presence of a substrate) 

As it changes shape it puts a strain on the substrate and this distorts the bond or bonds in the substrate and lowers the activation energy needed to break the bond. 

Drawn Model: 

• A rise in temp increases the kinetic energy and as a result the particles move around more rapidly and collide more often
• In a cataysed reaction the enzyme and substrate molecules come together more often in a given time 
• However as the temperature rises the hydrogen and other bonds in the enzyme being to break, this mean the enzyme and its active site change shape and the substrate fits less easily slowing the rate of reaction (this is at 45 degrees) 
• Denaturation= permanent change and it cannot function again after this has occured as the enzyme is so disrupted 

It is a measure of its hydroyen ion concentration. 

The increase or decrease of pH reduces the rate of enzyme action. 

pH affects how an enzyme works in these ways: 

• A change means a change on the amino acids that make up the active site, so the substrate can no longer become attached to the active site 
• May cause th bonds maintaing the tertiary structure to break and the active site therefore changes shape 

If you increase the enzyme concentration the substrate will be acted on and the rate of reaction will increase. 

However if the substrate is limiting (cannot supply all of the enzymes) there will be no effect on the rate of reaction. 

Graph: 

Low substrate concentration mean the enzymes only have a limited number of them to act on/ collide with. However the more you add the faster it will reach the highest point until it will have no effect. 

Figure 8 (p30): 

Nucleotide Structure:

3 compounents:

• Pentose Sugar 
• Phosphate Group 
• Nitrogeous organic base (CTUAG)

All of these 3 components are combined from a condensation reaction= single nucleotide (mono)

Bond between the sugar and phosphate= phosphodiester bond (joining nucelotides) 

• Polymer made up of nucleotides 
• Pentose sugar= ribose 
• single, short chain
• Organic bases= A, G, C and U 

• Pentose sugar= deoxyribose 
• Organic Bases= A,T,G and C 
• Made up of two stands of nucleotides (joined by hydrogen bonds formed between bases) 
• Long chains

Bases on the DNA strands are joined by hydrogen bonds. 

Base pairs: 

• A-T
• C-G

These bases are complimentary to each other 

Ratios between AT and GC but this can vary between species. 

It is stable because: 

• Phosphodiester backbone protects the more reactive bases inside the double helix 
• Hydrogen bonds link the base pairs by forming bridges 
• Interactive forces between the bases (base stacking) 

There are 3 hydrogen bonds between C and G= the more C-G pairs= the more stable the DNA molecule is. 

There are a infinitate number of sequences for bases that provides genetic diversity. 

Adapted to carry out its function by: 

• It hardly mutates (passes gentics on without changing)
• Hydrogen bonds that are weak means its easy for them to be unzipped in DNA replication and protein synthesis 
• Base pairing means DNA is able to replicate and transfer information as mRNA 

The function of DNA depends of the sequence of base pairs. 

Two main ways: 

• Nucleur Division: mitosis and meiosis 
• Cytokinesis: whole cell divides 

Before it divides the DNA has to be replicated. This is to ensure that all the daughter cells have the gentic material to produce enzymes and other proteins needed. 

Requirements for it to happen: 

• All bases present 
• Both strands must act as templates for attachments of nucleotides 
• Enzyme= polymerase
• Chemical energy 

Takes place as follows: 

• DNA helicase breaks the hydrogen bonds 
• Double helix separates and unwinds 
• The exposed polynucleotide acts as a template to which complimentary free nucleotides bind by specific base pairing 
• Joined in condensation reaction by enzyme DNA polymerase 
• Each new DNA contains one of the original DNA stands (half the orginal DNA has been saved. 

Semi-conserative= half the original DNA has been saved and built into each of the new DNA molecules. 

Role of DNA polymerase in the semi-conservative replication of DNA: 

Uses:

• Metabolic processes 
• Movement 
• Active sites 

Advantages:

• Short term release of energy (glucose takes longer)
• Unstable high energy bonds 
• Cannot be stored so has to be continuosly made in the mitroncondria 

Made up of: adrenine( nitrogenous base), ribose (5 carbon ring), phosphates chain (3) 

Phosphate Bonds: bonds are unstable and release lots of energy 

Hydroysis reaction: (draw)

Condensation Reaction: (draw)

• Dipolar: oxygen is negetive charge and hydrogen is postively charge; has both postive and negetive poles
• The attractive force between the oxygen and hydrogen is called a hydogen bond (fairly weak) 
• it takes alot of heat to separate it (high boiling point), 
• Water acts as a buffer against sudden temperature variations 
• Hydroyen bondsing between water means it takes alot of energy to evaporate it= latent heat of vaporation 
• Evaporation of sweat means cooling because body heat is used to evaporate water to help maintain body temperature 
• Cohesion= tendency of molecules to stick together (the hydrogen bonds) 
• Surafce tension= water molecules are pulled back into the body rather than escaping meaning small organisms can be supported on top of the water 

Metabolism: 

• breaking down of molecules via hydroysis and is produced in condensation reactions 
• Raw material of photosynthesis 

Solvent: (dissolves)

• ammonia and urea 
• inorganic ions such as amino acids