Skills: Molecules (DP IB Biology: HL)

Drawing biological molecules

• It is important to be able to draw a few key molecules
  • There is a huge variety of biological molecules, but only the most important ones are required

• Element symbols from the Periodic Table are used
• A short, straight line is used for a covalent bond, with two lines for a double bond
• Some chemical groups may be denoted by a symbol such as ℗ for a phosphate group
• The symbol R represents a variable chemical group, such as the variable side groups of amino acids
• An exam question may require you to draw various molecules
• It's advisable to break the task down into stages

Symbols Used in Biological Molecule Drawings Table

Drawing α-D-glucose

• Aspects to remember
  • Glucose has the formula C₆H₁₂O₆
  • In solid form, glucose has a linear structure
  • It forms a hexagonal ring in an aqueous solution
    • As aqueous glucose is the only state that glucose exists in biology, it's the ring structure that should be learned

  • One of the corners of the ring (draw this in the top-right) is occupied by an oxygen atom
  • The 6th carbon occupies a side chain (top-left)
  • The carbon atoms are numbered 1 to 6 starting on the right and working clockwise
  • The hydroxyl groups occupy positions above or below the ring as follows
    • Carbon atom 1 - below
    • Carbon atom 2 - below
    • Carbon atom 3 - above
    • Carbon atom 4 - below

• You can ignore the 'D' in the names alpha-D-glucose or beta-D-glucose
  • The only other version is L-glucose which plays no significant role in biology

Recommended steps to draw a molecule of α-D-glucose

Structure of α-D-glucose

β-D-glucose is very slightly different in structure

• Beta-glucose (β-glucose) has a small, subtle difference to α-glucose
• The hydroxyl group on carbon atom 1 sits ABOVE the ring, rather than below
• This sugar is the monomer of cellulose
• This example of two different isomers changes the properties of the polysaccharide formed from these monomers drastically
  • It accounts for all the many differences between starch and cellulose

• The hydroxyl groups occupy positions above or below the ring as follows
  • Carbon atom 1 - above
  • Carbon atom 2 - below
  • Carbon atom 3 - above
  • Carbon atom 4 - below

Structure of β-D-glucose

Drawing a ribose sugar

• This family of sugars play a role in DNA and RNA structure, as well as ATP
• Ribose is a form of pentose sugar (5 carbon atoms)
• Like glucose, ribose has a ring structure
• Aspects to remember
  • Ribose has the formula C₅H₁₀O₅
  • It forms a pentagonal ring in an aqueous solution
  • One of the corners of the ring (draw this in the top) is occupied by an oxygen atom
  • The 5th carbon occupies a side chain (top-left)
  • The carbon atoms are numbered 1 to 5 starting on the right and working clockwise
  • The hydroxyl groups occupy positions above or below the ring as follows
    • Carbon atom 1 - above
    • Carbon atom 2 - below
    • Carbon atom 3 - below

• Ribose sugars have an important close relative - deoxyribose sugars
  • Both are key components of RNA and DNA respectively
  • The 'R' and 'D' of RNA and DNA comes from the sugar in the structure, ribose or deoxyribose

Recommended steps to draw a molecule of ribose

Structure of ribose

Drawing a saturated fatty acid

• There are two aspects to a saturated fatty acid
  • A saturated hydrocarbon chain
    • Contains only C-C single bonds
    • Each internal carbon atom is bonded to 2 hydrogen atoms

  • A carboxylic acid group at one end

• You don't need to memorise any names of saturated fatty acids
  • The number of carbon atoms in your chain is also not important, but greater than around 8 is advised.

Recommended steps to draw a molecule of a saturated fatty acid

A saturated fatty acid

Drawing a generalised amino acid

• Each amino acid has central carbon atom
• Three of the bonds from the central carbon atom are occupied as follows
  • a hydrogen atom
  • a carboxylic acid group
  • an amine group

• The fourth bond attaches the central carbon to the R group
  • The R group is variable and determines the identity of the amino acid
  • You won't need to remember any of the R groups or amino acid names

• Drawing the 4 groups surrounding the central carbon in a flat structure is acceptable, although the real arrangement of bonds around a carbon atom is in a tetrahedral shape

Recommended steps to draw a molecule of generalised amino acid

The generalised structure of an amino acid

• As well as being able to draw certain molecules, an important skill is being able to recognise certain biochemicals from molecular diagrams
• There are several features that help to identify molecules
• The presence of carbon, hydrogen, oxygen, nitrogen, sulfur and phosphorus can help in the identification
• All biological macromolecules contain carbon, hydrogen and oxygen
• Nitrogen and sulfur are present in proteins
• Nitrogen is present in nucleic acids (DNA, RNA)
• Phosphorus is also present in certain molecules (DNA, RNA and phospholipids)
• The presence of ring structures, hydrocarbon chains, carbon-to-carbon double bonds, double-stranded areas and the ratio of carbon to oxygen in a molecule all give clues about the molecule's identity

Using the Presence of Various Atoms to Identify Biochemicals

• Glycosidic bonds, ester bonds and peptide bonds all have a distinctive appearance in molecular drawings and will immediately identify carbohydrates, lipids and proteins respectively

Step 1: Look at the elements present in all the diagrams

We're looking for a triglyceride, a type of lipid. Lipids contain C, H and O only. B also contains nitrogen (B is a dipeptide)

Eliminate Answer B

Step 2: Look for lipid structures

A contains ring structures, so is likely a carbohydrate (A is a disaccharide)

Eliminate Answer A

Step 3: Look for three hydrocarbon chains

D contains three hydrocarbon chains (attached by ester bonds to glycerol). C is cholesterol, which is a lipid, but not a triglyceride lipid.

Select Answer D

The ratio of hydrogen to oxygen

• • The numbers of hydrogen and oxygen atoms in a molecule can help to identify it
  • Carbohydrates contain hydrogen and oxygen in a 2:1 ratio
    • Think of water, formula H₂O, and where the '-hydrates' part of the word 'carbohydrates' comes from

  • Lipids contain a much lower proportion of oxygen than carbohydrates eg. C₁₈H₃₄O₂, where the hydrogen to oxygen ratio is 17:1

• Having learned to draw the structure of a generalised amino acid, two or more of these can be joined together to show how peptide bonds form during protein synthesis
• Amino acid monomers link together via a condensation reaction
  • This releases a molecule of water (H₂O)
  • One H atom (of the released water) comes from one amino acid's amine group
  • The other H atom and an O atom come from the other amino acid's carboxylic acid group

• This knowledge can be useful when drawing how two amino acids condense to form a peptide bond

The recommended steps in drawing a peptide bond formation

Formation of a dipeptide