IB Biology SL

Revision Notes

2.1.1 Molecules

Molecular Biology

The substances of life

  • There are 118 elements in the Periodic Table
  • Only the first 92 elements occur in Nature – the rest are artificially-synthesised in laboratories and are very unstable
  • Only around 21 elements are required for life
    • The rest have no role in sustaining life (some are poisonous eg. arsenic)
    • Some elements can be used in medicine eg. titanium for skeletal implants, thanks to its inertness, lightness and strength
  • There are 4 ubiquitous elements in biological systems
  • These 4 make up over 96% of living matter
    • Oxygen – 65% of body mass (humans)
    • Carbon – 18%
    • Hydrogen – 10%
    • Nitrogen – 3%
  • Other trace elements found in organic compounds are: bromine, calcium, chlorine, chromium, copper, iodine, iron, magnesium, manganese, molybdenum, phosphorus, potassium, selenium, silicon, sodium
  • There are other trace elements found in certain phyla only e.g. strontium in certain corals (Cnidaria)

Elements in biology exist mainly in compounds

  • Such compounds are mainly covalent compounds
    • Electrons are shared between atoms to generate strong bonds within compounds
    • For example, elemental carbon only exists as graphite and diamond, which are of no direct use to organisms
    • Carbon forms millions of different covalently-bonded compounds, mainly with hydrogen and oxygen
    • Oxygen is absorbed in elemental form but is quickly converted to its compounds during transportation and respiration
  • Some are ionic eg. sodium chloride
  • Some elements form prosthetic groups with larger organic molecules eg. magnesium in chlorophyll, iron in haemoglobin

All of Biology can be explained at a molecular level

  • The molecules in cells, and the elements that go to form them, are the basis of all events that occur in Nature
  • Everything that is observed has a molecular explanation
  • Imagine an all-powerful ‘zoom lens‘ that could look into any level of detail of life
  • Such a lens could start at its most zoomed-out, looking at our biosphere, the Earth
    • We assume that alien life does not exist because we haven’t found evidence for it yet
  • We see habitats, populations, communities and individual organisms coming into view in that order, as we zoom in
  • As we zoom in on one organism, we enter its body and see increasing levels of detail, right down to the molecular level
  • The zoom model helps understand the important interfaces between chemistry, biology and physics
  • We could zoom in further, to look at sub-atomic particles, although that begins to enter into the realms of physics!

Synthesis of Organic Molecules

The link between chemistry and biology

  • In the early 1800s, the theory of vitalism stated that a living force, a mysterious non-molecular entity, was necessary for all life
  • Frederick Wöhler, a German physician, was the first to synthesise a biological molecule, urea, from inorganic compounds.
  • Wöhler heated ammonium cyanate and produced urea, a well-known organic constituent of blood and urine
    • Urea had been thought to be found only in living organisms
  • The formation of urea from ammonium cyanate helped to disprove the theory of vitalism, which has been completely falsified by subsequent findings
  • All of the observations of biology now have a molecular explanation, and that is now universally accepted

Carbon

Carbon’s unique chemistry makes it the ideal basis of living systems

  • Carbon has 4 electrons in its outer (second) shell
  • Carbon can form 4 strong covalent bonds using these 4 electrons
  • Covalent bonds are strong so can form very stable, large molecules
  • Carbon can bond to another carbon, or other atoms such as hydrogen, nitrogen, oxygen, sulfur and the halogens
  • Carbon can form long-chain and cyclic compounds which are stable and allow a very high number of possible organic compounds to exist
  • Carbon’s four bonds form a tetrahedral structure, which allows the formation of stereoisomers, which have different 3-D shape and hence, different biological properties
  • Carbon can form double and triple bonds to an adjacent carbon atom, allowing unsaturated compounds to form
  • Carbon can form part of (and join onto) many different functional groups that give organic compounds their individual properties
    • Alcohol groups
    • Hydroxyl groups
    • Ketone groups
    • Aldehyde groups
    • Carbonyl groups
    • Amino groups
    • Sulfhydryl groups
    • Phosphate groups

Carbon Compounds

  • The key molecules that are required to build structures that enable organisms to function are:
    • Carbohydrates
    • Proteins
    • Lipids
    • Nucleic Acids
    • Water
  • All of these except water contain carbon

5 Biological molecules (1), downloadable IGCSE & GCSE Biology revision notes5 Biological molecules (2), downloadable IGCSE & GCSE Biology revision notes

The key biological molecules for living organisms

  • Carbohydrates, proteins, lipids and nucleic acids contain the elements carbon (C) and hydrogen (H) making them organic compounds
  • Carbon atoms are key to the organic compounds because:
    • Each carbon atom can form four covalent bonds – this makes the compounds very stable (as covalent bonds are so strong they require a large input of energy to break them)
    • Carbon atoms can form covalent bonds with oxygen, nitrogen and sulfur
    • Carbon atoms can bond to form straight chains, branched chains or rings
  • Carbon compounds can form small single subunits (monomers) that bond with many repeating subunits to form large molecules (polymers) by a process called polymerisation
  • Macromolecules are very large molecules
    • That contain 1000 or more atoms therefore having a high molecular mass
    • Polymers can be macromolecules, however not all macromolecules are polymers as the subunits of polymers have to be the same repeating units

Carbohydrates

  • Carbohydrates are one of the main carbon-based compounds in living organisms
  • All molecules in this group contain C, H and O
  • As H and O atoms are always present in the ratio of 2:1 (eg. water H2O, which is where ‘hydrate’ comes from) they can be represented by the formula Cx (H2O)y
  • The three types of carbohydrates are monosaccharides, disaccharides and polysaccharides

Types of Carbohydrate Table

Types of carbohydrate table, downloadable AS & A Level Biology revision notes

Exam Tip

When discussing monomers and polymers, you should be able to give the definition and also name specific examples eg. nucleic acids – the monomer is a nucleotide.

The Two Forms of Glucose

  • The most well-known carbohydrate monomer is glucose
  • Glucose has the molecular formula C6H12O6
  • Glucose is the most common monosaccharide and is of central importance to most forms of life
  • There are different types of monosaccharide formed from molecules with varying numbers of carbon atom, for example:
    • Trioses (3C) eg. glyceraldehyde
    • Pentoses (5C) eg. ribose
    • Hexoses (6C) eg. glucose
  • Glucose exists in two structurally different forms – alpha (α) glucose and beta (β) glucose and is therefore known as an isomer
    • This structural variety results in different functions between carbohydrates

The Two Forms of Glucose, downloadable AS & A Level Biology revision notes

Straight chain and ring structural formula of alpha & beta glucose

  • Different polysaccharides are formed from the two isomers of glucose

Structure of polysaccharides table

Table 4 The two forms of glucose, downloadable AS & A Level Biology revision notes

 

Exam Tip

You must be able to recognise and draw the isomers of α and β glucose.

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