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