QCEChemistry

Organic materials: structure and function

Proteins

appreciate that organic materials including proteins, carbohydrates, lipids
and synthetic polymers display properties including strength, density and
biodegradability that can be explained by considering the primary, secondary
and tertiary structures of the materials

describe and explain the primary, secondary (a-helix and B-pleated sheets),
tertiary and quaternary structure of proteins

recognise that enzymes are proteins and describe the characteristics of
biological catalysts (enzymes) including that activity depends on the structure
and the specificity of the enzyme action

- The monomer of a protein is an amino acid

• Amino acids are organic compounds with both amine (-NH2) and carboxyl (-COOH) functional groups.
• General formula - H2N-CH(R)-COOH
• Consists of side chain which varies dependent on the amino acid - has significant impact on properties of amino acid and protein. The side chain can be:

▪ Non-polar (alanine)

▪ Polar (serine)

▪ Proton donors (aspartic acid)

▪ Proton acceptors (lysine)

• Amino acids are zwitterions (or dipolar ions)

▪ -NH2 group can act as base (accepting proton to become a -NH3+ group)

▪ -COOH group can act as an acid (donating proton to become a -COO- group)

▪ Amino acid present in cationic form in solutions of low pH and anionic form in solutions of high pH

▪ Reversible reaction - in aqueous solution of amino acid, there is equilibrium mixture amino acid molecules and zwitterions

Primary structure

- Primary structure of protein is the sequence of amino acids, joined by peptide bonds

• A peptide is a polymer made of amino acid monomers
• A polypeptide is a large peptide containing many amino acids
• Condensation reaction links amino acids, and water is produced as a by-product (condensation polymerisation reaction)
• Proteins are large polypeptide chains with >50 amino acids

▪ Function of proteins is highly dependent on the order of amino acids

Explanation: why do proteins fold into 3D structures?

- Two main reasons - minimise repulsion, maximise attraction between amino acids and surroundings

• Hydrophobic effect - folding of protein to 'bury' non-polar amino acids within the interior to shield them from water. Polar amino acids exist on the surface of the protein, so interactions with the water take place
• Non-polar amino acid interactions - hydrophobic interactions
• Polar neutral amino acids interact through hydrogen bonding
• Polar acidic and basic amino acids interact through ionic bonds, salt bridge
• Cysteine amino acids interact through sulfur atoms interact in disulfide bridge

Tertiary structure

- Tertiary structure is the 3D interactions between numerous secondary structures present in a polypeptide

• Folding due to the IMF and interactions of the side chains

▪ Non-polar side chains - dispersion forces (hydrophobic)
▪ Polar - dipole-dipole or H-boning (hydrophilic)
▪ Ionic - electrostatic interactions (soluble)
▪ Disulfide bridge - covalent bonding (between nearby sulfur containing side chains

• With increasing strength of IMF, increase density, increased solubility and increased strength of protein
• e.g. myoglobin

Quaternary structure

- Quaternary structure is the folding of multiple protein chains together

• Determines shape and function of protein
• All folding is disrupted by excessive heat and either basic or acidic conditions
• e.g. hemoglobin

Enzymatic catalysis

- Enzymes are a biological catalyst, which reduce the activation energy for a reaction

• Provides alternate pathway by allowing molecules to 'collide' in the right orientation ('lock and key' mechanism), and/or a differing reaction mechanism based on intermediate reactions with the side chain
• Active side is an indentation in the protein structure (enzyme) that binds the substrate

- Differences between inorganic catalysts and enzymes

• Enzymes only catalyse one specific reaction with a particular bond or functional group, while inorganic catalysts can catalyse many different reactions
• Enzymes are more sensitive to changes in reaction conditions

▪ Lose catalytic activity outside pH and temperature range

▪ This is because proteins 3D structure is affected by pH and temperature

What does "all folding is disrupted by excessive heat
and either basic or acidic conditions" mean?

When you increase the temperature, the kinetic
energy will increase. Excessive vibrations will
eventually breakdown the IMF’s holing the protein
together. The weakest will break first. It is the IMF’s
that are holding the molecule in a particular shape
allowing it to work as a catalyst. As the pH changes,
the NH group can act as a base, along with the side
chains that can accept or donate a proton. This
changes/disrupts the existing IMF’s therefore
denaturing the protein.

Carbohydrates

appreciate that organic materials including proteins, carbohydrates, lipids and synthetic polymers display properties including strength, density and biodegradability that can be explained by considering the primary, secondary and tertiary structures of the materials

recognise that monosaccharides contain either an aldehyde group (aldose) or a ketone group (ketose) and several -OH groups, and have the empirical formula CH 0

distinguish between a-glucose and B-glucose, and compare and explain the structural properties of starch (amylose and amylopectin) and cellulose

Carbohydrates are natural occurring sugars and their polymers

- They are polyhydroxy aldehydes or ketones, and the molecules they form through condensation

• Empirical formula CH2O
• Structure can be represented as straight chain (Fischer Projection), ring structure (Harworth Projection or chair structure - 3D structure)
• Intermolecular forces - H-bonding and dipole-dipole with many hydroxyl groups (very soluble in water and very high melting points)

- Monosaccharides

Monosaccharides are single sugar monomers

• General formula CxH2yOy
• Glucose (C6H12O6) is a common monosaccharide - aldehyde (aldose), 6 membered ring (hexose), source of energy for cells
• Fructose (C6H12O6) - ketone (ketose), 5 membered ring (pentose)

Disaccharides

• Joins through condensation reaction between two hydroxyl groups to form a glycosidic bond - a bond that connects sugar monomers together)
• Maltose - 2 alpha glucose
• Sucrose - alpha glucose + fructose
• Lactose - galactose and beta glucose

Polysaccharides

• Form when monosaccharides undergo condensation polymerisation
• Insoluble due to large size

Liquids

appreciate that organic materials including proteins, carbohydrates, lipids
and synthetic polymers display properties including strength, density and
biodegradability that can be explained by considering the primary, secondary
and tertiary structures of the materials

recognise that triglycerides (lipids) are esters and describe the difference in
structure between saturated and unsaturated fatty acids

describe, using equations, the base hydrolysis (saponification) of fats
(triglycerides) to produce glycerol and its long chain fatty acid salt (soap),
and explain how their cleaning action and solubility in hard water is related to
their chemical structure

A type of lipid is triglycerides

- Triglyceride is made from glycerol (alcohol) and 3 fatty acids

• Structure of fatty acids determine the properties of the triglyceride Saturated fatty acids have hydrocarbon chains with only single carbon-carbon bonds (general formula - CnH2n+1COOH) (stearic acid)
• Monounsaturated fatty acids contain one carbon-carbon double bond in the hydrocarbon chain (general formula - CnH2n-1COOH) (oleic acid)
• Polyunsaturated fats contain more than one carbon-carbon double bond in the hydrocarbon chain (linoleic acid)
• Increasing unsaturation (more double bonds) - cause bending - pack less tightly therefore lower melting point
• Increasing carbon chain length - increased dispersion forces therefore higher melting point.

- Condensation reaction

Explanation: why are saturated fats bad for the body, compared to unsaturated fats?

- Saturated fats are very stable and do not easily react with other molecules

• Made from single covalent bonds in carbon chain - do not react with acids or bases, alcohols, amines or metals
• Only strong oxidisers such as chlorine gas or oxygen in burning reactions can break the bond
• As a result, saturated fatty acids oxidise in the body with difficulty

▪ Acidic group at end of fatty acid is reactive, and allows for oxidation of the chain by cutting it to pieces, two carbons at a time

- An unsaturated fat is more chemically active, and is much more readily oxidised by the body

Soaps

- Saponification (or base hydrolysis) is the organic reaction between an acidic ester and a strong base to produce a fatty acid salt

- Soaps are amphipathic - have both hydrophobic and hydrophilic parts

• Called surfactants - surface acting agent or emulsifying agents - allow emulsions to form between water and non-polar substances
• 
• Hydrophobic means water hating - dispersion forces with other tails - can form dispersion forces with non-polar solvents like oil
• Hydrophilic means water loving - dipole-dipole and hydrogen bonds with other heads - can form dipole-dipole interactions with polar solvents

- Cleaning action

1. Soap dissolves in water
2. Dirt and grease are hydrophobic so are attracted to hydrophobic part of molecules (hydrophobic tail is in grease and hydrophilic head in water
3. Soap breaks dirt or grease into smaller particles and agitation lifts grease from surface
4. Dirt particles can dissolve in water because the surface of each dirt particle contains only the hydrophilic heads of soap molecules (forming micelles)

- Micelles

• Micelles are spherical arrangements of soap ions clustered together (contain 40-100 tails)

▪ Pick up dirt by forming around the grease droplets, allowing them to form an emulsion in water

▪ Micelles repel other micelles. Allowing them to be stable.

Hard water

- In hard water (containing dissolved Ca+2 and Mg+2) - sodium stearate (soap) is soluble but calcium and magnesium are not and precipitate as scum

• More soap is required to have the same cleaning capacity as in soft water
• Can use detergent - has similar cleaning mechanism to soap, but does not precipitate out in hard water

explain how the properties of polymers depends on their structural features
including; the degree of branching in polyethene (LDPE and HDPE), the
position of the methyl group in polypropene (syntactic, isotactic and atactic)
and polytetrafluorethene.