Biological molecules

• Hydrogen bonds form between water molecules because water is polar: oxygen is more electronegative than hydrogen, so it attracts electron density in the covalent bond more strongly. This forms O delta negative and H delta positive, leading to intermolecular forces of attraction between a lone pair on O delta negative of one molecule and H delta positive on an adjacent molecule
• Biologically important properties of water:

  • Reaches maximum density at 4 ℃
  • High surface tension
  • Incompressible
  • Metabolite/solvent for chemical reactions in the body
  • High specific heat capacity
  • Higher boiling point than expected
  • Cohesion between molecules
• The incompressible nature of water is important for organisms because it provides turgidity to plant cells and a hydrostatic skeleton for some small animals like earthworms
• Ice floats on water because it is less dense than water due to hydrogen bonds holding molecules in fixed positions further away from each other. This is important for organisms as it insulates water in arctic climates, allowing aquatic organisms to survive, and water acts as a habitat
• The high surface tension of water is important for organisms because it slows water loss due to transpiration in plants, allows water to rise unusually high in narrow tubes, lowering demand on root pressure, and enables some insects to 'skim' across the surface of water
• Water is an important solvent for organisms because it is a polar universal solvent that dissolves and transports charged particles involved in intra and extracellular reactions, such as PO4^3- for DNA synthesis
• The high specific heat capacity and latent heat of vaporisation of water are important for organisms because they act as a temperature buffer, enabling warm blooded animals to resist fluctuations in core temperature to maintain optimum enzyme activity. Water also has a cooling effect when it evaporates from the skin surface as sweat or from the mouth when panting
• Monomer: smaller units that join together to form larger molecules. Examples include monosaccharides (glucose, fructose, galactose, ribose), amino acids, and nucleotides.

  Polymer: molecules formed when many monomers join together. Examples include polysaccharides, proteins, and DNA/RNA
• In condensation reactions, a chemical bond forms between two molecules and a molecule of water is produced. In hydrolysis reactions, a water molecule is used to break a chemical bond between two molecules, such as peptide bonds in proteins and ester bonds between fatty acids and glycerol in lipids
• Elements found in carbohydrates and lipids: C, H, O. Elements found in proteins: C, H, O, N, S. Elements found in nucleic acids: C, H, O, N, P
• alpha-glucose and beta-glucose are both hexose monosaccharides (6C) with ring structures. Alpha-glucose is a cis isomer, while beta-glucose is a trans isomer
• Properties of alpha-glucose:

  • Small and water-soluble for easy transport in the bloodstream
  • Complementary shape to antiport for co-transport for absorption in the gut
  • Complementary shape to enzymes for glycolysis as a respiratory substrate
• Ribose is a pentose monosaccharide (5C) with a ring structure
• When monosaccharides react, a (1,4 or 1,6) glycosidic bond forms. Two monomers form one chemical bond, resulting in a disaccharide, while multiple monomers form many chemical bonds, resulting in a polysaccharide
• Three disaccharides and how they form:

  • Maltose: glucose + glucose
  • Sucrose: glucose + fructose
  • Lactose: glucose + galactose

  All have a molecular formula of C12H22O11 and are formed through a condensation reaction that forms a glycosidic bond between two monosaccharides
• Structure and functions of starch:

  • Storage polymer of alpha-glucose in plant cells
  • Insoluble with no osmotic effect on cells
  • Large and does not diffuse out of cells
  • Made from amylose (1,4 glycosidic bonds) and amylopectin (1,4 & 1,6 glycosidic bonds, branched for hydrolysis into glucose)
• Structure and functions of glycogen:

  • Main storage polymer of α-glucose in animal cells
  • Contains 1,4 & 1,6 glycosidic bonds
  • Branched for hydrolysis
  • Insoluble with no osmotic effect and does not diffuse out of cells
  • Compact
• Structure and functions of cellulose:

  • Polymer of beta glucose that gives rigidity to plant cell walls
  • Prevents bursting under turgor pressure and holds stem up
  • Contains 1,4 glycosidic bonds
  • Straight-chain, unbranched molecule
  • H-bond crosslinks between parallel strands form microfibrils with high tensile strength
• Triglycerides form through a condensation reaction between one molecule of glycerol and three fatty acids, forming ester bonds
• Contrast between saturated and unsaturated fatty acids:

  Saturated:

  • Contain only single bonds
  • Straight-chain molecules with many contact points
  • Higher melting point, solid at room temperature
  • Found in animal fats

  Unsaturated:

  • Contain C=C double bonds
  • 'Kinked' molecules with fewer contact points
  • Lower melting point, liquid at room temperature
  • Found in plant oils
• Structure of triglycerides related to their functions:

  • High energy: mass ratio for high calorific value from oxidation
  • Insoluble hydrocarbon chain for waterproofing
  • Slow conductor of heat for thermal insulation
  • Less dense than water for buoyancy of aquatic animals
• Structure and function of phospholipids:

  • Amphipathic with glycerol backbone, 2 hydrophobic fatty acid tails, and 1 hydrophilic polar phosphate head
  • Forms phospholipid bilayer in water as a component of membranes
  • Tails can splay outwards for waterproofing
• Phospholipids and triglycerides are not polymers; they are macromolecules
• Structure and function of cholesterol:

  • Steroid structure of 4 hydrocarbon rings
  • Hydrocarbon tail and hydroxyl group (-OH)
  • Adds stability to cell surface phospholipid bilayer by connecting molecules and reducing fluidity
• General structure of an amino acid: amino group (NH2), carboxyl group (COOH), hydrogen atom, and R group (side chain)
• General structure of an amino acid:

  • COOH: carboxyl/carboxylic acid group
  • R: variable side group consists of carbon chain & may include other functional groups e.g. benzene ring or -OH (alcohol)
  • NH2: amine/amino group
• Polypeptides form through condensation reactions between amino acids forming peptide bonds (-CONH-)
• Primary structure of a protein:

  • Sequence, number & type of amino acids in the polypeptide, determined by sequence of codons on mRNA
• Two types of secondary protein structure:

  • alpha - helix:
  • All N-H bonds on the same side of the protein chain
  • Spiral shape
  • H-bonds parallel to helical axis
  • beta - pleated sheet:
  • N-H & C=O groups alternate from one side to the other
• Tertiary structure of a protein:

  • 3D structure formed by further folding
  • Disulfide bridges: strong covalent S-S bonds between molecules of the amino acid cysteine
  • Ionic bonds: relatively strong bonds between charged R groups
  • Hydrogen bonds: numerous & easily broken
• Quaternary structure of a protein:

  • Functional proteins may consist of more than one polypeptide
  • Precise 3D structure held together by the same types of bond as tertiary structure
  • May involve addition of prosthetic groups e.g. metal ions or phosphate groups
• Structure and function of globular proteins:

  • Spherical & compact
  • Hydrophilic R groups face outwards & hydrophobic R groups face inwards = usually water-soluble
  • Involved in metabolic processes e.g. enzymes such as amylase, insulin, haemoglobin
• Structure of haemoglobin:

  • Globular conjugated protein with prosthetic group
  • 2 alpha-chains, 2 beta-chains, 4 prosthetic haem groups
  • Water-soluble so dissolves in plasma
  • Fe2+ haem group forms coordinate bond with O2
  • Tertiary structure changes to facilitate subsequent O2 binding (cooperative binding)
• Structure and function of fibrous proteins:

  • Can form long chains or fibres
  • Insoluble in water
  • Useful for structure and support e.g. collagen in skin
• Functions of collagen, elastin, and keratin:

  • Collagen: component of bones, cartilage, connective tissue, tendons
  • Elastin: provides elasticity to connective tissue, arteries, skin, lungs, cartilage, ligaments
  • Keratin: structural component of hair, nails, hooves/claws, horns, epithelial cells of outer layer of skin
• Test for proteins in a sample (Biuret test):

  • Confirm presence of peptide bond
  • Add equal volume of sodium hydroxide to sample, then add drops of dilute copper (II) sulfate solution
  • Positive result: color changes from blue to purple
• Test for lipids in a sample:

  • Dissolve solid samples in ethanol, then add an equal volume of water and shake
  • Positive result: milky white emulsion forms
• Test for reducing sugars:

  • Add an equal volume of Benedict’s reagent to a sample, then heat the mixture in an electric water bath at 100 ℃ for 5 mins
  • Positive result: color changes from blue to orange & brick-red precipitate forms
• Benedict’s test for non-reducing sugars:

  • Negative result: Benedict’s reagent remains blue
  • Hydrolyze non-reducing sugars e.g. sucrose into their monomers by adding HCl, then neutralize and proceed with the Benedict’s test
• Test for starch:

  • Add iodine solution
  • Positive result: color changes from orange to blue-black