Chapter 2: Biological Molecules

Molecular biology: The study of biological molecules 

Metabolism: The sum total of all the biochemical reactions in the body 

• Catabolism - breaks down 
• Anabolism - synthesis of complex molecules
• Metabolism is complex but has an underlying simplicity
• Has a close relationship between the structure and their functions 

The building blocks of life 

• Hydrogen, carbon, oxygen and nitrogen 
• Monomers - single repeating units that are joined to form polymer 
• Macromolecules - giant molecule made from many repeating units. 
• Types of reaction: 
• Condensation - Removal of water 
• Hydration - Addition of water 
• Polysaccharides - food storage/ structural purposes
• Nucleic acid and proteins are informational molecules 

Monomers	Polymers
Monosaccharides	Polysaccharides
Amino acids	Proteins
Glycerol & fatty acids	Lipids
Nucleotides	Nucleic acid

Carbohydrates (CHO) 

Monosaccharides (glucose, galactose, fructose) 

• Sweet-tasting 
• Single surgar molecules 
• Glucose is a respiratory substrate. Broken down to provide energy in the form of ATP 
• Build blocks for larger molecules 
• Ring structures 
• Alpha glucose (used to form starch) 
• Beta glucose (form cellulose) 

Disaccharides (maltose, lactose, sucrose) 

• Formed by joining two monosaccharides 
• Scurose - transport from leaf to growing point of stem and roots (phloem) 
• Lactose - from milk 
• Maltose - from germinating barley for brewing
• Joining two monosaccharides takes place by condensation 
• Reverse of condensation is addition of water, known as hydrolysis  
• Forms glycosidic bond 
• Carbon atom 1 of one monosaccharide and carbon atom 4 of the other 
• 1,4 glycosidic bond 

Polysaccharide 

• Convenient, cannot be crystallized, compact and insoluble 
• Starch is a mixture of 2 substances 
• Amylose (20%) 
• Straight chain by 1,4 glycosidic bonds 
• Chains are curved and coiled up into helical strctures like springs so as to make the molecule more compact 
• Stores energy more efficiently 
• Amylopectin (80%)
• Highly branched chain by 1,4 and 1,6 glycosidic bonds 

• Large starch grains in chloroplasts 
• Potato tubers 
• Starch easily seen using light microscope 

• Glycogen 
• Shorter chains than amylopectin 
• High metabolic activity 
• Easily hydrolysed to alpha-glucose 
• Blood glucose concentration 
• Glycogen granules in animal cells, liver and muscle cells

• Cellulose
• Straight, unbranched chains run parallel to one another, allowing hydrogen bonds to form cross-linkages between adjacent chains 
• Forms cell wall 
• High tensile strength 
• Prevents cell from bursting because water eneters by osmosis 
• When drawing:
• 180 degrees rotation for glucose molecules 
• H bond inside molecules 
• H bond between molecules 
• Cellulose, hemicellulose, pectin, lignin
• Hemicellulose - short chain of carbohydrate acting as glue binding to each other and cellulose molecules 
• Pectin - polysaccharide acts as glue and holds the cell walls of neighboring cells together 
• Lignin - covalently cross link to cellulose and hemicellulose 
• 60 to 70 cellulose molecules tightly cross-links to form microfibrils, then to fibres 

Characteristics	Amylose	Amylopectin	Glycogen	Cellulose
Found in	Plants	Plants	Animals and fungus	Plants
Found as	Grains	Grains	Tiny granules	Fibres
Function	Energy store	Energy store	Energy store	Structural support
Basic monomer	Alpha glucose	Alpha glucose	Alpha glucose	Beta glucose
Type of bonds	1,4 glycosidic	1,4 & 1,6 glycosidic	1,4 & 1,6 glycosidic	1,4 glycosidic
Type of chain	Unbranched and helical	Long, few branches	Shorter, many branches	Long, unbranched with no coiling

Dipoles and hydrogen bonds 

• Covalent vond - shared pair of electrons

Lipids (CHO)

• Triglycerides Fatty acids (-COOH)
• Greater H:O ratio than carbohydrate 
• Insoluble in water, organic molecules 
• Soluble in organic solvent such as alcohol and acetone 
• Ester bond through condensation/ polymerisation reaction 

Saturated (Single bond)	Unsaturated (Double bond)
Solid at room temperature, fatty acid tails fold	Liquid at room temperature, fatty acid tails cannot fold
Higher melting point	Lower melting point
Exist as FAT	Exist as OIL
Energy source Buoyancy Insultation	Energy source

• Alcohols and esters (-OH)
• Acid + alcohol produces ester
• -COOH + -OH and forms -COO- 
• Condensation reaction
• Triglycerides 
• 3 fatty acids tails and three ester bonds 
• Insoluble in water 
• Soluble in ether, chloroform, ethanol 
• Non-polar are the hydrocarbon tails
• No uneven distribution of charge, so does not mix with water molecules 
• Good energy source - provides more than twice as much as carbohydrate 
• Insulation
• Buoyancy 
• Metabolic source of water 
• When oxidised in respiration, they are converted to carbon dioxide and water 
• Camels and kangaroo rats survive 
• Phopholipids
• One of the 3 fatty acids replaced by a soluble phophate group 
• Hydrophobic tails and hydrophilic head 
• Glycerol + 2 fatty acid tails 

Proteins 

• Amino acids 
• Amine + carboxylic acid -NH2 + -COOH 
• Hydrogen atom (H) and R group 
• 20 different amino acids 
• Amino acid --> Dipeptide --> Polypeptide 
• Peptide bond 
• A carbon atom of the first amino acid free to bond with the nitrogen atom of the second 
• Condensation reaction - formation of glycosidic bonds 
• Dipeptide - 2 linked amino acids 
• Hydrolysis - Addition of water 
• Ribosomes are the sites where amion acids are joined together to form polypeptides 
• Primary Structure 
• The sequence of amino acids in a polypeptide chain 
• Simple protein consists of a single polypeptide chain 
• Thousands of amino acids form a polypeptide chain 
• Secondary Structure 
• Simple protein consists of a single polypeptide 
• A structure resulting from the regular coiling or folding of the chain of amino acids 
• Alpha-helix
• Beta-pleated sheet 
• Polypeptide chains linked in parallel flat sheet, straighter and smoother shape 
• H bonds form between C=O and NH groups of adjacent chains 
• Random coil 
• Due to hydrogen bonding between the oxygen of -CO- group and the hydrogen of -NH- group 
• Easily broken by high temperatures and pH changes 
• Tertiary Structure 
• Compact structure of protein molecule resulting from the 3D coiling of the already-folded chain of amino acids 
• 4 different bonds 
• Disulphide bond (polar) 
• Ionic bond (acid & base)
• bonds are weaker than disulfide bridges, broken down by pH changes 
• Hydrogen bond (polar)
• Attraction between electronegative oxygen atom on the C=O groups and electropositive hydrogn atom of NH groups. Individually weaker than ionic bonds but large number makes them able to maintain the tertiary structure 
• Hydrophobic interactions (non-polar)
• Non-polar R groups in amino acids, repel water 
• Come into close contact and exclude water
• Quaternary Structure 
• 3D arrangement of 2 or more polypeptide chains 
• Due to attracton of 2 R groups 
• Haemoglobin has 4 polypeptide chains 
• 2 alpha-globin chain 
• 2 beta-globin chain 
• Haem group - 2alpha 2beta 
• Total of 4 haem group = 4 oxygen molecules = 8 oxygen atoms 

Fibrous protein	Globular protein
Repetitive regular sequences of amino acids (Gly-Pro-Ala)	Irregular amino acids sequences
Actual sequences may vary slightly	Never varies, highly specific
Long parallel strands	Spherical shape
Vary in length for two same example of protein	Identical length for two same proteins
Stable molecule (H-bond covalently twist)	Unstable molecule
Support and structural functions Collagen and keratin	Metabolic functions (carries oxygen) Enzymes, hormones, haemoglobin

• Haemoglobin - a globular protein 
• Oxygen-carrying respiratory pigment 
• Ability to transport oxygen 
• Ball shape - compact shape 
• Hydrophobic interactions fo groups within the haemoglobin molecule 
• Hydrophilic groups in the molecule tend to orient themselves to point outwards 
• A haem group - part of protein moelcule but not made of amino acids - prosthetic group --> contains Fe2+
• Each Fe2+ ion combines with a single oxygen molecule 
• Total 4 oxygen molecules carried by a single haemoglobin molecule 
• Haemoglobin + oxygen --> Oxyhaemoglobin (bright red) 
• Collagen - a fibrous protein 
• Unbranched polypeptide chain 
• Collagen moelcule is made up of 3 polypeptides 
• Small and compact - helix wound tightly 
• Larger amino acids lead to more loosely wound and less strong helix 
• Triple-stranded molecules run parallel forming fibres 
• 3 strands held together by H bonds and some covalent bonds 

Water 

• Hydrogen bonding 
• Dipole-dipole attraction interaction 
• Water as a solvent 
• Polar and ionic substances dissolve readily in water 
• Water as a transport medium 
• Transports blood, lymphatic, excretory and digestive 
• Xylem transports water and solutes from roots to leaves 
• High specific heat capacity 
• Large amount of heat is required to raise temperature 
• More stable habitats for aquatic organisms 
• High latent heat of vaporisation 
• A large amount of heat energy is lost for relatively little lost of water 
• Sweating 
• Cools down body --> transfers large amount of energy 
• Density and freezing properties 
• Liquid less dense than solid 
• Aquatic organisms survive in ponds as it freezes from top down 
• High surface tension and cohesion (tendency of molecules to stick together)
• Water surface acts like a skin and xylem vessel in plants 
• Water has large cohesive forces and allow to be pulled up through xylem vessels 
• Surface tension - water molecules at the urface tend to be pulled back into the body 
• Water as a reagent 
• Chemical reactions inside the cells