Biological Molecules

• Condensation reactions
  • Join monomers together into larger molecules, releasing water
  • Monosaccharides → Disaccharides → Polysaccharides: glycosidic bonds formed
  • Amino acids → Polypeptides: peptide bond
  • Glycerol + fatty acids → Triglycerides: ester bonds

• Made up of monosaccharides (monomers of carbohydrates)
• Common monosaccharides - glucose, galactose, fructose
• Disaccharides
  • Formed by condensation reaction of 2 monosaccharides
  • Maltose → Glucose + Glucose
  • Sucrose → Glucose + Fructose
  • Lactose → Glucose + Galactose

Two isomers:

• α-glucose: Carbon atom 1 has hydrogen pointing up, and hydroxyl group pointing down
• β-glucose: Carbon atom 1 has hydrogen and hydroxyl groups flipped

The acronyms 'ADDUD' and 'BUDUD' can be used to remember which way the -OH groups point. ADDUD - α-glucose, down, down, up, down. BUDUD - β-glucose, up, down, up down.

• Formed by condensation of many monosaccharides
  • Glycogen → condensation of α-glucose
  • Starch → condensation of α-glucose
  • Cellulose → condensation of β-glucose
• Structure of Glycogen
  • Energy store in animals
  • Highly branched structure, coiled – so compact
  • Unable to diffuse out of cells, so stays where it is needed until energy is required

• Structure of Cellulose
  • Unbranched, linear chains
  • Used in plant cell wall – provides rigidity to plants
  • Fibres group together to form microfibrils – hydrogen bonds (strength in large numbers)
• Structure of Starch
  • Forms granules – unable to move out of cells it is formed in – doesn’t have to diffuse far, so reasonably quick access to energy
  • Branched chains, coiled – compact

• Triglycerides
  • Glycerol + 3 fatty acid tails
  • Form oils, waxes, fats
  • Hydrophobic – do not mix with water

• Phospholipids
  • Form the cell wall – phospholipid bilayer
  • Phosphate + glycerol + 2 fatty acid tails
  • Polar molecules – phosphate head is hydrophilic (water loving) // fatty acid tails are hydrophobic (water hating)

• Fatty acids
  • Saturated – all carbon atoms have single bonds – with the maximum number of hydrogens possible
  • Unsaturated
    • Monounsaturated – 1 pair of carbon atoms have a double bond; removes 2 hydrogens, causes a kink in the chain
    • Polyunsaturated – More than 1 pair of carbon atoms have a double bond; removes more than 2 hydrogens, causes many kinks in the chain
    • Have less energy content than unsaturated fatty acids

• Made up of amino acids

• Amine group: NH2 Carboxyl group: COOH
• R group – the side chain causing the amino acid to be unique
• Dipeptides – condensation of two amino acids
• Polypeptides – condensation of many amino acids

• Proteins can be made up of multiple polypeptide chains

• Primary structure: order of amino acids – polypeptide chain

• Secondary structure: α-helix or β-pleated sheet – formed by hydrogen bonds between R-groups
• Tertiary structure: further coiling of α-helix / β-pleated sheet – more compact
• Quaternary structure: linking together of multiple tertiary structure polypeptide chains
• Hydrogen bonds – hold together the polypeptide chains in quaternary structure
• Ionic bonds – join together amino acids into polypeptide chain
• Disulphide bridges – strong bonds between R-groups holding α-helix / β-pleated sheet together

• Lower the activation energy of the reaction it catalyses
• Lock and Key model of enzyme action
  • Substrate fits perfectly in the enzyme
  • No explanation as to how the enzyme catalyses the reaction
• Induced Fit model of enzyme action
  • Enzyme active site changes shape slightly to allow the substrate to bind to it
  • Active site puts stresses on the substrate, causing bonds to brake
  • Reaction is catalysed, causing the product(s) to be released
• Enzymes are only able to have 1 substrate fit it – amylase only catalyses starch hydrolysis

• Enzyme concentration – a higher concentration will cause the substrate to be broken down faster. The rate of reaction will plateau as the substrate concentration decreases, as collisions are less likely to occur
• Substrate concentration – higher concentration of substrate means that the enzymes are more likely to collide with substrate. Increase rate of reaction, to a point. Once all of the enzyme has substrate in active site, reaction cannot continue further
• Inhibitor concentration – higher concentration of competitive inhibitors will cause reaction to slow, as more competitive inhibitor blocks active sites Non-competitive inhibitors will have an impact, however it is not based on concentration as they do not block the active site

• pH – outside of the enzymes optimum pH, the active site denatures quickly. This prevents the reaction from being catalysed
• Temperature – below the optimum temperature, the reaction slows, as less energy to cause collisions Above optimum temp – reaction stops – enzymes denature

• Genetic material for living organisms
• Adenine (purine), Thymine / Uracil (pyramidal), Guanine (purine), Cytosine (pyramidal)
• Semi-Conservative Replication
  • DNA unzips: DNA Helicase
  • Base pairs move in between the unzipped strands
  • DNA Polymerase used to bind the new bases to the old strands
  • Forms 2 DNA strands, each with 1 old strand and 1 new strand
• Proof for semi-conservative replication
  • DNA replicated until all Nitrogen is ¹⁵N – this is heavier, causing the strand to be lower in solution
  • DNA then replicated 1 generation with ¹⁴N – this creates a hybrid DNA, with 50% ¹⁵N and 50% ¹⁴N
  • DNA replicated 1 further generation in ¹⁴N solution – creating DNA with 25% ¹⁵N and 75% ¹⁴N
  • This is repeated, eventually forming DNA only containing ¹⁴N
  • The solution can be centrifuged, DNA containing different Nitrogen isotopes to be identified

• Used to transfer energy within cells
• Made of: Adenine, 3× Phosphate groups, Ribose sugar
• ${\displaystyle ATP+H_{2}O\rightarrow ADP+P_{i}}$ – condensation on ATP, forming ADP and a phosphate group; breaking the bond releases energy
• Low activation energy, so it is easy to release energy
• ATPase – enzyme catalysing hydrolysis of ATP (break down of ATP into ADP)
• Photophosphorylation
• Photosynthesis: Plants only, Using light to synthesise ADP → ATP
• Oxidative Phosphorylation
  • Using respiration to synthesise ADP → ATP; Plants and Animals
• Substrate-level Phosphorylation
  • When phosphate groups are transferred from donors; plants and animals
  • Uses of ATP
  • Metabolic Processes – provides energy to build up molecules from subunits
  • Movement – energy is required for muscular contraction
    • Active Transport – movement of molecules against a concentration gradient
    • Secretion – ATP is needed to form lysosomes to encase cell products
    • Activation of Molecules – inorganic phosphate released in hydrolysis of ATP can phosphorylate other molecules

• Essential for all living organisms
• Polar Molecule
  • Hydrogen bonds between water molecules require lots of energy to break
  • Causes water to have a high surface tension
• Solvent
  • As water is polar, other polar molecules are able to dissolve in it
  • Ionic compounds are surrounded by water molecules when dissolved
  • Allows gases to be dissolved – CO2, O2, NH3…
• High Specific Heat Capacity
  • A lot of energy is required to increase the temperature by 1° - this is due to the strength of the hydrogen bonds
  • This means that water acts as a buffer, reducing temperature fluctuations
• High Latent Heat of Vaporisation
  • A lot of energy is required to evaporate water (into steam)
  • Ideal for cooling an organism – sweating (animals) or transpiring (plants)
• Cohesion between Molecules
  • High surface tension means that column of water is able to be pulled up a vessel (such as a xylem)
• Metabolite
  • Used in condensation / hydrolysis reactions to break / form bonds

• Occur in solution in the cytoplasm / bodily fluids
• Some are in high concentrations, others in low concentrations
• Each ion has a specific role
  • Iron ions Haemoglobin
  • Sodium ions co-transport of Glucose and Amino Acids
  • Phosphate ions Part of DNA and ATP