Monday, March 31, 2014

Biomolecules (Synthesis of Biomolecules)

- Synthesis of very large molecules (macromolecules) from small sub-units called monomers
- Monomers join together using covalent bonds
- Condensation reaction (sometimes known as dehydration synthesis)
- For every one bond formed, one molecule of water is released
- All 4 types of biomolecules are made through condensation reaction


For every one bond formed, one molecule of water is released


Overview of Condensation Reaction
Monomer (s)
Polymer Formed
By-product
Bond Name
Monosaccharide (simple sugar)
Disaccharide (di-sugar) à Polysaccharide (complex sugar)
Water
Glycosidic bond
Amino acid
Dipeptide à Polypeptide
Water
Peptide bond
Glycerol
Fatty acids
Monoglycerides
Diglycerides
Triglycerides (Glycerol attached to fatty acids)
Water
Ester bond
DNA /RNA nucleotides
DNA
RNA
Water
Phosphodiester bond

Biomolecules (Synthesis of Nucleic Acids)

- Monomers: DNA and RNA nucleotides
- In DNA replication, each new strand that forms is built up from nucleotides, joined by repeated condensation reactions (polynucleotide chains)




Biomolecules (Hydrolysis Reaction)

The splitting of a polymer by adding water to a covalent bond
- Catalyzed by a hydrolyses enzyme

Biomolecules (Properties of Water)

1. Water as a Solvent

  • Many solvents are dissolved in the water of biological fluids (e.g. Blood plasma)
  • Hydroophilic substances dissolve in water and this is important for:
    • Transport - Blood plasma consists of about 90% water and is used to dissolve a wide range of useful substances and waste products which can then be easily transported
  • Secretion – Most secretions comprise substances in aqueous solution. E.g. digestive juices contain enzymes in solution

2. Thermal Properties of Water

  • Water has high heat capacity
    • A lot of heat is required to increase or decrease its temperature by 1 degrees Celsius
    • Water can act as a thermal buffer, i.e. it can resist large changes in temperature
    • Allow for thermoregulation
  • Water has high heat of vapourization
    • A lot of heat can be lost with negligible loss of water from the body
    • This is important for regulating the body temperature of organisms
  • Water has high heat of fusion
    • A lot of heat must be lost before water freezes
    • Contents of cells are less likely to freeze. Ice crystals are extremely damaging if they develop within cells

3. Density and Freezing Properties

  • Water is most dense at 4°C
  • As water at the surface of a pond decreases from 4 degrees Celsius to 0 degrees Celsius, its density decreases and it remains at the surface and then it freezes
  • Water molecules are more closely packed in liquid water than in solid ice. This explains why ice is less dense than water at 0 degrees Celsius
  • Hence, water in ponds freezes from the top downwards. The layer of ice insulates the water below, preventing complete solidification

4. Cohesion and Surface Tension

  • Cohesion is the force of attraction between like molecules. The cohesion of water molecules is due to the hydrogen bonds between them
  •  One effect of the cohesive forces in water formation is surface tension. It is surface tension that allows insects to walk on the surface of water
    • Tendency of molecules of a liquid to stick together at the surface due to its polarity and hydrogen bonding
5. Adhesion Forces

  • Adhesion is the force of attraction between unlike molecules
  • Large adhesive forces exist between the cellulose walls of xylem vessels and the water within them
  • Adhesive forces play a role in maintaining a column of water in xylem vessels
  • Capillary action
    • The tendency of a liquid substance to move along the surface of solid substance due to adhesion (as in water climbing a glass tube or inside a tree), even in spite of gravitational or other forces acting in the opposite direction

6. Penetration by Light Rays

  • In clear water, red and yellow light can reach a depth of 50m while blue and violet can penetrate 200m deep
  • The ability of light to penetrate water enables photosynthetic organisms to occupy the vast volumes of lakes and oceans
  • Light can easily penetrate the water-filled epidermis of leaves and reach the underlying mesophyll cells, which contain chloroplasts  

7. Water has Low Viscosity

  • Examples of lubricating fluids which are predominantly water:
    • Mucus is used externally to aid movement in animals (e.g. snail and earthworm). It is also used internally in the movement of food along the digestive tract or movement of sperm along the oviduct
    • The synovial fluid lubricates movement in many vertebrate joints
    • The pericardial fluid lubricates movement of the heart  

8. Metabolic Role of Water

  • Water is required for the hydrolysis of many substances (e.g. proteins, lipids and carbohydrates)
  • All biochemical reactions in cells occur in an aqueous medium
  • Water is needed for the diffusion of materials across surfaces such as in leaf cells
  • Water acts as a substrate for photosynthesis

Biomolecules

- All life is cellular
- All living things are from 50 to over 90% water, the source of protons, hydrogen and oxygen in photosynthesis and the solvent of biomolecules
- The major elements of covalently bound biomolecules are carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P) & sulfur (S)
- There is a universal set of small molecules (i.e. sugars, amino acids, nucleotides, fatty acids, phospholipids, vitamins and coenzymes)
- The principle macromolecules are proteins, lipids, carbohydrates and nucleic acids
- There is a universal type of membrane structure (the lipid bilayer)

Organic Molecules vs Biomolecules
- Carbon was a major component, found in any type of organism that was analyzed
- Molecules with carbon in them were assumed to be associated with organisms, and so were called organic molecules
- Elements like H, O, N and S can also be found in organic molecules
- Many of the biomolecules contain carbon, and thus, can be referred to organic compounds as well
- 4 different types of organic molecules 

  • Lipids
  • Carbohydrates
  • Proteins
  • Nucleic Acids