biomolecules and water

• Important functional groups in biological molecules:

  • effectively all are polar and hydrophilic
  • Hydroxyl - many in carbs
  • carbonyl
  • carboxyl - (carboxylic acid) present in amino acids and fatty acids
  • amino
  • ester - ester bonds in lipids and nucleic acids (organic)
  • phosphate
  • Methyl - methyl/hydrocarbon (non-polar/ hydrophobic)
• organic: (contain carbon and hydrogen)

  • macromolecules = molecules containing a very large number of atoms, many of which are polymers: chain of repeating units called monomers joined together by a covalent bond through a condensation reaction e.g. carbs, DNA and starch
  • small molecules - many of which are monomers = a molecule (repeating unit) that can be covalently bonded to other similar/identical molecules to form a polymer
• The composition of a living cell:

  • 70% water
  • 1% inorganic substances
  • 29% organic polymers and other macromolecules
  • 0-1% organic monomers and other organic molecules
• Calcium ions (cations, inorganic): Ca 2+

  • part of bone and enamel structure as calcium phosphate
  • a cofactor in blood clotting
  • an ion involved in nerve transmission across the synapse and in muscle contraction
• Sodium ions (cations, inorganic): Na+

  • an electrolyte
  • essential function in nerve transmission
  • essential in water reabsorption in loop of Henle and collecting duct
• Potassium ions (cations, inorganic): K+

  • an electrolyte
  • essential function in nerve transmission
  • essential in water reabsorption in loop of Henle and collecting duct
  • used in plant guard cells as part of stomatal opening mechanism
• Hydrogen ions (cations, inorganic): H+

  • involved in hydrolysis and condensation reactions
  • involved in ATP formation
  • involved in control of blood pH and in transport of carbon dioxide
• Ammonium ions (cations, inorganic): NH4 +

  • an intermediate ion in the deamination of proteins
• Nitrate (anions, inorganic): NO3 -

  • nitrogen source for green plants manufacture proteins; it is the form taken up from the soil
• Hydrogen Carbonate (anions, inorganic): HCO3 -

  • involved in carbon dioxide transport in the blood, with H+
• Chloride (anions, inorganic): Cl-

  • the shift of chloride ions into and out of red blood cells maintains pH balance during carbon dioxide transport
• Phosphate (anions, inorganic): PO4 3-

  • as phospholipids, phosphates form part of cell membranes
  • forms calcium phosphate, an important constituent of bone forgiving strength
  • constituent of ATP and nucleic acids
• Hydroxide (anions, inorganic): OH-

  • involved in hydrolysis and condensation
• The interconversion of POLYMERS AND MONOMERS:

  HYDROLYSIS:

  • all polymers are broken down/hydrolysed into their respective monomers by the addition of water to break the covalent bond

  CONDENSATION REACTION:

  • all monomers are joined together/ condensed/ polymerised into their respective polymers by the removal of water to form the covalent bond
• • Condensation: an anabolic reaction, endothermic (requires an input of energy)
  • hydrolysis: Catabolic reaction, exothermic (releases energy)
• Carbohydrates:

  • polymer: polysaccharide
  • name of bond between monomers: glycosidic bond
  • monomers: monosaccharides
  • elements (choose from C,H,O,N,S,P): CHO
• Fats/lipids:

  • polymer: triglyceride
  • name of bond between monomers: ester bond
  • monomers: 3 fatty acids and glycerol
  • elements: CHO
• Proteins:

  • polymer: Polypeptide
  • name of bond between monomers: peptide bond
  • monomers: amino acids
  • elements: CHONS
• nucleic acids (DNA/RNA):

  • polymer: polynucleotide
  • name of bond between monomers: phosphodiester bond
  • monomers: (mono) nucleotides
  • elements: CHONP
• Biological importance of water:

  • 2/3 of globe
  • 70% of humans
  • freezes at 0 C
  • boils at 100 C
• Oxygen has a much more positively charged nucleus than hydrogen

  electrons more attracted to oxygen -> polar molecule (unequal distribution of charge in a charge polar molecule

  delta negative: slightly (electro) negative

  delta positive: slightly (electro) positive

  A) 8 protons

  B) 1 proton

  
• Polar:

  • a molecule or functional group that has an unequal distribution of charge e.g. water
  • also, functional groups of biological molecules which include: -OH, -NH2, -C=O
• Hydrogen bonds:

  • electrostatic attraction between a slightly positively charged hydrogen of one water molecule and the slightly negatively charged oxygen of a neighboring water molecule
  • bonds can form: between water molecules, between water and other polar or charged molecules as well as between dif. polar functional groups
  • weaker than covalent and ionic bonds
• ion:

  • an atom or a molecule that has an unequal number of protons and electrons
• Hydrophilic:

  • a molecule/ substance attracted to water
  • polar or charged molecules
• hydrophobic:

  • a molecule/ substance repelled by water
  • also known as non-polar
  • non-polar molecules are lipid soluble and composed of -CH3 and -CH2 functional groups
• solvent:

  • a liquid in which substances are dissolved
• solute:

  • a substance dissolved in a liquid
• solution: a liquid composed of a solute dissolved in a solvent
• Water is polar:

  • known as the universal solvent as it dissolves more substances than any other liquids, it forms a shell around ions and makes H bonds with polar solutes
  • water is a medium for chemical reactions to take place
  • cells of both eukaryotes and prokaryotes are 70% water. Solutes of cells are polar or charged
  • water acts as a transport medium e.g. in blood, phloem and xylem
  • water is the reactant for some reactions e.g. hydrolysis
• high specific heat capacity:

  • SHC: amount of heat energy (KJ) required to raise the temp of 1 kg of a substance by 1C
  • high for water because of hydrogen bonds
  • stable temp for enzyme controlled reactions
  • both eukaryotic and prokaryotic cells are less prone to damage from changes in environmental temp.
  • aquatic organisms have stable environment
  • thermoregulation is facilitated for organisms that maintain their constant temp
• High latent heat of vaporisation:

  • LHV: amount of heat energy required to turn 1kg of a substance in liquid state to gaseous state
  • High for water bec of hydrogen bonds between molecules
  • water as a coolant
  • sweat evaporating off skin
  • panting and gaping
  • transpiration stream keeps the leave cool in hot weather
• density of ice and water:

  • in ice, each water molecule is hydrogen-bonded to a maximum (4) of other water molecules. crystal structure formed requires water molecules to move further apart from each other. therefore, there are fewer water molecules in a given space than in liquid water. makes ice less dense than water and it floats on water (highest density of water is at 4C)
  • ice insulates ponds - water remains liquid underneath enabling aquatic life to survive
  • forms a habitat for terrestrial organisms on its surface in cold habitats
  • nutrients are circulated
• cohesive forces/ cohesive tension:

  • property of the surface of a liquid that allows it to resist an external force formed on water due to high cohesive forces (H bonds)
  • habitat for insects e.g. pond skater
• adhesive forces/ adhesion:

  • attraction of molecules of one kind for molecules of a dif. kind e.g. water and glass, allows for capillarity
  • water movement in transpiration stream enabled by its attraction to xylem walls
• transparent: light will penetrate to reach aquatic plants and algae for p/s
• gametes can be suspended - sperm can reach eggs for both internal and external fertilisation
• living things contain a lot of water - they are at an equivalent density - buoyancy for aquatic organisms
• high latent heat of fusion (much heat must be removed before it freezes) - contents of cells and aquatic environments are slow to freeze
• hard to compress - provide a hydrostatic skeleton