2.1.2. Biological molecules

• Hydrogen bonds are weak forces of attraction. They can form between water molecules or between parts of a larger molecule. In water there is attraction between the oxygen of one molecule and the hydrogen of another molecule.
• This attraction occurs because each water molecule is polar, which means there is an uneven distribution of charge. Oxygen atoms attract electrons more strongly than hydrogen atoms. Therefore, the electrons in a water molecule are pulled towards the oxygen atom, which gives the oxygen end of the molecule a more negative charge. This is shown as delta negative (δ–). The hydrogen end of the molecule is left with a delta positive (δ+) charge. It is these opposite delta charges that attract the water molecules together, producing hydrogen bonds.
• Hydrogen bonds cause cohesion. Between 0°C and 100°C, they hold water molecules together loosely — they are held together, but they can move past one another and the water remains a liquid. In order to evaporate, the hydrogen bonds must be broken, allowing the molecules to separate and form a gas (water vapour). This takes a lot of energy, so water remains a liquid up to 100°C.
• At lower temperatures the molecules have less kinetic (movement) energy and move about less. With less movement, more hydrogen bonds can form and at 0°C enough hydrogen bonds have formed to hold the water molecules in a stationary position, forming ice. The water molecules are now held in a formation known as an open lattice, which holds the molecules further apart. Therefore, ice floats as it is less dense than water.
• • Thermal stability — water has a high shc which means that a lot of energy is needed to warm it up. A lot of energy is required to overcome the force of its hydrogen bonds between the molecules. Therefore, a body of water maintains a fairly constant temperature. Aquatic organisms can then use less of their energy on temp control. Internal body temp changes slowly, so fairly stable, reducing variations in metabolic rate that would otherwise occur with temperature change. This also allows gases to remain soluble in water.
• • Freezing — ice is less dense than water as it forms an open lattice structure so it floats, forming an insulating layer on the water and preventing the water below the ice from freezing.This means that the organisms beneath the ice do not freeze and nutrients can still circulate. The ice itself can also act as a habitat for organisms such as polar bears.
• • Evaporation — Water has a high latent heat of vaporisation. Therefore, a lot of energy is needed to cause a liquid to change into a gas (evaporation), which is an efficient mechanism used to cool the surface of living things. This energy is known as latent heat. An example of where this is used is sweating.
• • At most temperatures water is a liquid — it can flow and transport materials in living things.
• • Cohesion — the attraction of water molecules to each other, and produces surface tension, which creates a habitat on the surface for invertebrates such as pond skaters. It also enables continuous columns of water to be pulled up the xylem.
• • Transparent- this allows aquatic plants to carry out underwater photosynthesis
• • High density-- this allows water to support organisms and allows for flotation
• • Solvent — as the molecules are polar, water can dissolve a wide range of substances, and thus can transport substances around the body. It allows ionic compounds like magnesium chloride to separate into their charged ions, and so dissolve in water as they are able to interact with it. This allows organisms such as fish to take up said ions from the water. Water can thus act as both an external and an internal transport medium, and can be used to dilute toxic substances.
• • As a reactant — water molecules are used in a wide range of metabolic reactions such as hydrolysis and photosynthesis.
• • Incompressibility — water cannot be compressed into a smaller volume. This means it can be pressurised and pumped in transport systems or used for support in hydrostatic skeletons.
• Hydrogen bonds are present in the alpha helices and beta pleated sheets of the secondary structure of protein, water, in protein tertiary structure, between polypeptide chains in quaternary structures of proteins like haemoglobin, between chains of cellulose, and between bases in DNA.
• In nucleic acids, the monomers are nucleotides. They are made up of a:

  • A phosphate group
  • A pentose sugar
  • An organic base
• There are five different bases. These are adenine, cytosine, guanine, thymine and uracil (replaces thymine in RNA), which are usually abbreviated to A, C, G, T and U.
• In proteins, the monomers are amino acids. There are 20 different amino acids used to build proteins. The different sequences that these amino acids can be used in provide huge diversity in protein structure.
• The monomers in both complex carbohydrates and proteins are joined by covalent bonds created by a condensation reaction. A condensation reaction is when two molecules join to become one larger molecule via the formation of a covalent bond and the release of a water molecule.The bond can be broken again via hydrolysis.
• Carbohydrates consist of carbon, oxygen and hydrogen. The general formula for a carbohydrate is (CH2O)x. Carbohydrates can be divided into three main groups: monosaccharides, disaccharides and polysaccharides.
• What are monosaccharides?

  These are the single sugar units that are used as monomers to build other carbohydrates. They are soluble and sweet reducing sugars

  Glucose has 6 carbons, and thus has the formula C6H12O6, and so only contains carbon, hydrogen and oxygen. There are two types of glucose, α-glucose and β-glucose. They have the same formula, but different structures (see diagram right). Glucose is used as a respiratory substrate to provide energy for the formation of ATP.
• Pentose monosaccharides contain five carbons, e.g. ribose and deoxyribose.
• Hexose monosaccharides contain six carbons, e.g. glucose.
• The difference between α-glucose and β-glucose is simply the position of the –H and –OH groups on the first carbon atom. (ABBA)
• fibrous proteins

  • insolvable, elongated rope strands, strong and touch, flexible
  • used for structure e.g. collagen in bone/ cartilage/ connective tissue, keratin in skin/ hair/ nails and fibrin for protection
  • it gives elasticity in blood vessels/ alveoli/ cartilage
  • used in contraction through actin and myosin in muscle
  • microtubules in cilia/ flagella/ spindle/ cytoskeleton
• globular proteins

  • soluble, spherical, have a 3D structure, conjugated and contain a prosthetic group, temperature/ pH sensitive, hydrophilic outside

  lol
• • enzymes with a metabolic role/ catalyse reactions by lowering the activation energy
  • hormones/ receptors for cell signalling e.g. insulin for blood glucose regulation
  • opsonin for phagocytes to bind to pathogens, agglutinins to cause pathogens to aggregate together, anti-toxins by binding to toxins and neutralising them, fibrinogen in blood clotting
  • transport substances across the cell membrane by being a carrier/ channel/ pump
  • transport substances in blood e.g. haemoglobin carrying oxygen
  • DNA is too large too leave the nuclear envelope