Molecules

• Water


  Makes up about 80% of the cells contents, it is the environment for the chemical reactions of life. The molecular structure and properties are unusual. Two hydrogen atoms are combined with an oxygen atom by sharing of electrons. The three atoms form a triangle, not a straight line. Within the molecule the oxygen nucleus draws electrons away from the hydrogen nuclei. So overall the water molecule is electrically neutral, but there is a net negative charge on the oxygen atom and a net positive charge on both the hydrogen atoms. A molecule carrying such an unequal distribution of electrical charge is called a polar molecule.
• Importance of water


  • Metabolism
  • Solvent
  • Lubricant
  • Supporting Role
  • Homeostasis
  • Fertilisation
• Metabolism


  • Hydrolysis (polymers to monomers)
  • Medium for chemical reactions
  • Diffusion and osmosis across surface
  • Substrate for photosynthesis

  
• Solvent


  Water readily dissolves other substances and is therefore used for transport, removal of wastes, and secretions
• Lubricant


  • Synovial fluid (lubricates joints)
  • Mucus (lubricates gut wall)
  • Pleural fluid (found between lungs and ribs)
• Supporting Role


  • Hydrostatic skeleton – Annelids
  • Turgor pressure in plants
  • Humours of the eye – Aqueous and vitreous
  • Medium in which to live
• Homeostasis


  Temp control due to its high specific heat capacity
• Fertilisation


  Fertilisation and dispersal in mosses and ferns
• Essential Inorganic Ions


  • Potassium
  • Calcium
  • Magnesium
  • Iron
  • Hydrogen carbonate
  • Nitrate
  • Phosphate
• Potassium


  As an enzyme cofactor / in maintaining osmotic equilibrium
• Calcium


  Calcium pectate binds adjacent cell walls in plants
• Magnesium


  Acts as a prosthetic group in chlorophyll / activates many enzymes
• Iron


  The prosthetic group in haemoglobin
• Hydrogen carbonate


  Transport of CO2 / buffer in blood
• Nitrate


  Constituent of proteins, nucleic acids, ATP and ADP
• Phosphate


  In cell membranes as phospholipids / ATP and ADP / nucleotides / and as buffers
• Buffers


  Compounds which act to resist small changes in pH on addition or dilution of moderate amounts of acid or alkali
• Cells and tissues can only function properly at or around neutrality and cannot tolerate significant changes in pH</b>
• Buffers act to mop up +ve or -ve charged ions which can affect pH
• Proteins


  Make up about 66% of the total dry mass of a cell. They contain the elements carbon, hydrogen, oxygen, nitrogen and usually sulphur. Most proteins are huge molecules, formed from amino acids combined in a long chain. Typically, several hundred or even thousands of amino acid molecules are combined together to make a protein. Once a chain is constructed, a protein takes up a specific shape. The shape of a protein is closely related to the function it performs.

  
• Amino Acids


  Carry two functional groups – a basic amino group (-NH2) and an acidic carboxyl group (-COOH). In the naturally occurring amino acids, both these groups are attached to the same carbon atom. The rest of the molecule, the side-chain or R-part, is very variable. Whilst amino acids have the same basic structure, they are all rather different in character. This is because they all carry different R-groups. (The R-group influences solubility, may act as a buffer and is involved in bonding that maintains secondary and tertiary structure)

  
• Bringing amino acids together in different combinations produces proteins with very different properties. This helps explain how the range of proteins in organisms are able to fulfil the very different functions they have

  
• Primary structure of a protein


  The arrangement of the long chain of amino acids in its molecule. Proteins differ in the variety, number and order of their constituent amino acids. In the living cell, the sequence of amino acids in the polypeptide chain is controlled by the coded instructions stored in the DNA of the chromosomes of the nucleus. Just changing one amino acid in the sequence of a protein may alter its properties completely.
• Secondary structure of a protein


  Parts of the polypeptide chain take up a particular shape immediately after formation at the ribosome. The most common shapes are formed either by coiling to produce an alpha helix or by folding into beta sheets. These shapes are permanent and held in place by hydrogen bonds.

  
• Tertiary structure of a protein


  The precise, compact structure that arises when the secondary structure is further folded and held in a particular complex 3D shape. This shape is made permanent by four different types of bonding established between different parts of the chains R groups. Some proteins take up a tertiary structure that is more spherical, and are called globular proteins. Most enzymes are globular proteins.

  
• The tertiary structure of a protein depends on its primary structure, as the bonds holding the tertiary structure can only form if the correct amino acids are at specific points along a polypeptide chain

  
• Bonding types and Interactions in proteins


  • Hydrogen
  • Ionic
  • Disulfide
  • Hydrophobic interactions
• Hydrogen bonds


  Numerous but relatively weak and easily broken
• Ionic bonds


  Formed between amino and carboxyl groups in some amino acid side groups. Stronger than hydrogen bonds they are damaged by pH changes.
• Disulfide bonds


  Covalent bonds between R-groups of sulfur-containing amino acids like cysteine. Very strong bonds with an important role in structural (fibrous) proteins like collagen.
• Hydrophobic interactions


  Involving amino acids with hydrophobic R-groups, which tend to take up positions within the molecule surrounded by other parts of the polypeptide, as opposed to water.

  
• Quaternary structure of protein


  Arises when two or more polypeptides become held together, forming a complex, biologically active molecule. An example is haemoglobin, which consists of four polypeptide chains held around a non-protein haem group. A group like this, which is an important, permanent, part of a protein molecule but is not made of amino acids, is called a prosthetic group. A protein that contains a prosthetic group is called a conjugated protein.

  
• Conjugated proteins


  • Glycoproteins, chlorophyll, myoglobin
• Types of proteins


  • Globular
  • Fibrous
• Globular proteins


  Have complex tertiary and sometimes quaternary structures. They are relatively unstable and are folded into spherical (globular) shapes such as myoglobin, haemoglobin, antibodies, hormones and enzymes. Their very specific shape results in the active site always being the same shape to form an enzyme/substrate complex with a specific substrate.

  
• Denaturation


  The loss of the specific 3-dimensional conformation of a protein molecule, but the amino acid sequence of the protein remains unaffected. If denaturation occurs, the bonds are broken and molecule unfolds, and can no longer perform its normal biological function.
• Fibrous proteins


  Examples are fibrin, collagen and keratin proteins which have no tertiary structure. They are long parallel polypeptide chains with occasional cross-linkages making up the fibres. They are stable, insoluble in water and very tough which makes them ideally suited to their mainly structural function within living organisms.
• Collagen


  A fibrous protein that is found in the skin, tendons, cartilage, bones, teeth and the walls of blood vessels. It is an important structural protein, not only in humans but in almost all animals. A collagen molecule consists of three polypeptide chains, each in the shape of a helix. The three helical polypeptides then wind around each other to form a three-stranded rope. Almost every third amino acid in each polypeptide is glycine. Its small size allows the three strands to lie close together and so form a tight coil. The three strands are held together by hydrogen bonds. Each complete 3 stranded molecule of collagen interacts with other collagen molecules running parallel to it. These cross-links (between R groups of lysine) hold many collagen molecules side by side, forming fibres. Collagen has tremendous tensile strength.
• Prions


  Disease causing proteins which act as self-propagating, infectious agents causing the spread of neurodegenerative disease like Scrapie in sheep, Bovine Spongiform Encephalopathy (BSE) in cattle and Creutzfeldt-Jakob Disease (CJD) in humans. These proteins can fold in multiple, structurally distinct ways as a result of changes in their secondary structure which gives a protein rich in tightly packed B-pleated sheets. These misfoldings are transmitted to other prion proteins leading to disease which is similar to viral infection.
• Routes of prion infection


  • Consumption of infected food
  • Open wound contaminated with soil or a medical procedure involving infected material i.e. transplant
  • Inheritance as a result of gene mutation occurring during meiosis in the production of an egg or sperm
  • Sporadically whereby spontaneous transformations occur converting normal proteins PrPc (2nd structure alpha helix) into disease causing forms PrPsc (2nd structure Beta sheets)