biological molecules

• water

  one atom of oxygen chemically bonded to two atoms of hydrogen

  • oxygen - small negative charge
  • hydrogen - small positive charge
  • because of these charge scientists say water is a polar molecule. the opposite charges mean water molecules are attracted to each other
• hydrogen bonds

  a hydrogen is formed between two or more water molecules. it is formed between the hydrogen atom on one water molecule and an oxygen atom on the other water molecule

  • weak bonds
  • in water the molecules are moving randomly, hydrogen bonds are still present
• properties of water

  very high specific heat capacity - put in or take out a large amount of energy to change the temperature

  • when water is heated the energy breaks or weakens the hydrogen bonds
  • temperature of water doesn't change rapidly so can act as a habitat for aquatic organisms - organisms could not function if water temperature changed rapidly. if water is frozen it turns to ice. ice insulates the water below and prevents it from freezing so therefore organisms can live in the water under the ice
• properties of water

  high latent heat of vaporisation - large amount of heat energy needed to evaporate water

  • allows organisms to cool themselves down without losing much water. e.g. sweating, heat energy is used to evaporate water from the surface of the skin and this transfer of energy allows the organism to cool down.
• roles of water - good solvent

  • water habitat (ponds and rivers) contains dissolved oxygen which is used by organisms living in the water to carry out respiration
  • transport substances (blood plasma) contains a large number of dissolved substances e.g. carbon dioxide, sodium ions, glucose and amino acids
  • transport substances in xylem vessels of plants, contains dissolved mineral ions (magnesium ions) pass into the roots from the soil. transported in the xylem from the roots to the leaves. then the magnesium ions are used to make chlorophyll for photosynthesis.
• roles of water

  • water molecules tend to stick together (cohesion). this is due to the hydrogen bonds between the water molecules. e.g. this allows for long columns of water to travel in the xylem tubes
  • cohesion also causes surface air tension where air meets water. allows the surface of water to act as a habitat (e.g. insects - pond skates)
• roles of water

  metabolic reactions

  water as a reactant - hydrolysis and photosynthesis

  water as a product - condensation and aerobic respiration
• glucose = C6H12O6
• glucose is a single sugar molecule - monosaccharide

  • mono = one
  • saccharide = sugar
• sugars with 6 carbon atoms are called hexose sugars

  sugars with 5 carbon atoms are called pentose sugars
• monosaccharides

  • soluble in water - this is because of the large number of OH groups (hydroxyl groups) so they form hydrogen bonds with water molecules and therefore soluble in water
  • hydrophilic - water loving and dissolvable
• monosaccharides can be chemically joined to form larger molecules

  • disaccharides
  • polysaccharides
• 2 forms of glucose (isomers)

  • alpha
  • beta
• in both isomers of glucose carbon 1 is bonded to a hydrogen atom and a hydroxyl group (OH group)

  the difference between alpha and beta glucose is the position of the hydroxyl group on carbon 1

  • alpha - OH group on carbon 1 is below
  • beta - OH group on carbon 1 is above
  • ABBA - alpha below beta above
• a disaccharide forms when two monosaccharides chemically react together

  • condensation reaction (lose water and a glycosidic bond is formed)
  • glycosidic bond between carbon 1 on one molecule and carbon 4 on the other molecule (1,4 glycosidic bond)
  • if water is added to the disaccharide the glycosidic bond is broken (hydrolysis reaction)
• disaccharides

  glucose + glucose = maltose

  glucose + fructose = sucrose

  glucose + galactose = lactose
• glucose is produced in plant cells using light energy trapped during photosynthesis

  • glucose is extremely soluble in water because it contains a large amount of hydroxyl groups. hydroxyl groups are polar due to the small negative charge on the oxygen and the small positive charge on the hydrogen so forms hydrogen bonds with water molecules making it soluble
  • if there is a large amount of glucose in the cell, water will move in by osmosis so therefore plants store glucose as starch as this is not soluble in water so water will not move into the plant by osmosis
• starch is found in plant cells in starch grains

  consists of 2 molecules

  • amylose
  • amylopectin
• amylose - polysaccharide

  • unbranched polymer of alpha glucose
  • contains thousands of alpha glucose molecules
  • joined by 1,4 glycosidic bonds which were formed in a condensation reaction
  • twists into a compact helix with hydrogen bonds forming between the glucose molecules along the chain
  • when a cell needs glucose water is used to break the glycosidic bonds (hydrolysis reaction)
• amylopectin - polysaccharide

  • branched polymer of alpha glucose
  • has a branch every 25-30 glucose molecules (another chain of alpha glucose molecules)
  • branch is connected to the main chain by a glycosidic bond - 1,6 glycosidic bond (carbon 1 of the above chain, carbon 6 of the below chain)
  • heavily branched molecule
• function of amylose and amylopectin

  • amylose is a compact tight helix so can store a lot of glucose molecules
  • insoluble in water, so means starch does not cause water to enter the cell by osmosis
  • amylose and amylopectin are too large to diffuse through the membrane and pass out of the cell
  • when a cell needs glucose, enzymes are used to break the glycosidic bonds (hydrolysis reaction and requires water). these enzymes break down and start at the ends of amylopectin, this is due to the branching (lots of ends) so enzymes can break down the starch rapidly
• structure of glycogen

  glycogen is found in animal cells as a store of glucose (found in liver and muscle tissues)

  • polymer of alpha glucose, joined by 1,4 glycosidic bonds
  • contains branches, glucose molecules at the branches are 1,6 glycosidic bonds
  • similar structure to amylopectin but glycogen is more branched, making it compact
  • large number of branches so has a lot of free ends, means the enzymes can concert glycogen back into glucose rapidly
• function of glycogen

  • if an animal needs to escape from a predator quickly, the rate of respiration would increase and glycogen in the animal muscles can be rapidly converted into glucose for respiration
  • glycogen is insoluble in water so does not cause water to move into the cell by osmosis
  • glycogen is large so cannot diffuse out of the cell

  these features make glycogen an ideal storage molecule in animal cells
• structure of cellulose

  • cellulose is part of the plant cell wall
  • polymer of beta glucose
  • every second molecule of beta glucose is inverted and a glycosidic bond is formed (1,4 glycosidic bond) - gives stability
  • unbranched polysaccharide
• function of cellulose

  • cellulose is a straight chain with no branching it allows the cellulose molecules to get close together and form hydrogen bonds between the chains. because there are a huge number of hydrogen bonds, this makes cellulose extremely strong
  • gives the plant strength, which allows it to carry out its functions
  • permeable to water molecules, water moves into the cell by osmosis so the plant contents push outwards against the cell wall, the strength of cellulose means it can resist the pressure and prevents the cell from bursting and keep its upright structure (turgid)
• cellulose

  • cellulose chains that group together are called microfibrils
  • microfibrils the group together and form large structure called macrofibrils
  • then macrofibrils group together and form a cellulose fibre, and cellulose fibres form the plant cell wall
• amino acids

  • all proteins are formed from amino acids
  • there are 20 different amino acids
  • many proteins consist of several polypeptides forming a large complex molecule
• structure of amino acids

  • 20 different amino acids
  • many proteins consist of several polypeptides forming a large and complex molecule
  • this is the general structure shared by all amino acids
  • amine and carboxyl group are the same for every amino acid, and the 'R' group is different for all of the 20 amino acids

  A) amine group

  B) carboxyl group

  C) 'R' group

  
• all proteins contain the same general elements

  • carbon
  • hydrogen
  • nitrogen
  • oxygen
  • some may contain sulphur
• peptide bonds

  • when 2 amino acids reacts together a peptide bond is formed. this creates a dipeptide
  • this is a condensation reaction and a molecule of water is created
  • if 3 or more amino acids are joined a polypeptide is created and one molecule of water is lost for every peptide bond formed
  • this reaction can be reversed by adding water and breaks the peptide bond (hydrolysis reaction) e.g. protease enzymes in the digestive system
• in order to be classed as a protein, a polypeptide has to fold into a complex 3D shape. once it has folded into the correct shape it can carry out its function (e.g. hormone or antibody)
• primary structure - order of amino acids

  the primary structure helps determine the final shape of the protein molecule, and the shape of the protein is critical for its function.

  • by changing a single amino acid can alter the shape of the final protein which can prevent it from carrying out its function effectively
• secondary structure - specific regions fold

  hydrogen bonds form all along the polypeptide between the amino acids. these can cause the polypeptide to fold and twists into shapes

  • alpha helix - twisted into a helical shape, held by hydrogen bonds
  • beta pleated sheet - folds into a flatter, sheet like structure and hydrogen bonds between the amino acids hold the sheet in place

  many proteins have regions of alpha helices and beta pleated sheets. the type of secondary structure formed depends on the primary structure in that region
• tertiary structure - overall 3D shape of a polypeptide chain

  • critical for how a protein functions e.g. active site of a enzyme, this depends on the protein forming a very specific tertiary structure. if the tertiary structure is changed (e.g. heating it) the shape of the active site changes and can no longer function effectively (denatured)
• quaternary structure - several polypeptide chains working together as a large molecule (e.g. haemoglobin, consists of 4 polypeptide chains (subunits))

  • only applies to proteins with at least 2 subunits
  • some proteins contain other non - protein molecules forming part of the structure (prosthetic groups) and help the protein to carry out its role (haemoglobin contains the prosthetic group haem which binds to oxygen)
  • proteins with prosthetic groups are called conjugated proteins
  • shows how the subunits are arranged and position of any prosthetic groups
• bonding in proteins

  these bonds form between the 'R' groups of the amino acids on a polypeptide chain
• bonding in proteins - hydrogen bonding

  amino acids containing a hydroxyl group means the slightly positive hydrogen and slightly negative oxygen means a hydrogen bond can form between the 2 'R' groups

  • contributes to the 3D shape of the polypeptide chain
  • weak bonds (easily broken by changes in temperature or pH)
• bonding in proteins - hydrophobic and hydrophilic

  several amino acids have uncharged 'R' groups (non polar amino acids) these are not attracted to water (hydrophobic) and hydrophobic amino acids tend to cluster together and exclude water molecules (hydrophobic interactions).

  • hydrophobic interactions tend to be found in the centre of an amino acid well away from water molecules
  • hydrophilic amino acids tend to be found on the surface where they can interact with water molecules
  • weak bonds
• bonding in proteins - ionic bonding

  • found between amino acids with charged 'R' groups
  • holds different parts of the polypeptide chain together
  • broken by changes in pH, this is why enzymes denature under acidic/alkali conditions
• bonding in proteins - disulphide bridges

  • forms between two sulphur molecules
  • type of covalent bond
  • relatively strong, not broken by changes in temperature or pH