1.4 Functional groups and reactivity

Learning Outcomes

  • Ability to identify common functional groups in biomolecules.

  • Explain how functional groups influence reactivity in biomolecules and the reactions they participate in.

  • Distinguish between heterolytic and homolytic reactions, and understand the role of free radicals in biological systems.

  • Focused understanding of how these concepts relate to biochemical reactions and biological processes.

Functional Groups in Biomolecules

  • The fundamental framework of biological molecules consists primarily of hydrocarbons.

  • Adding functional groups to these hydrocarbon structures modifies their physical and chemical characteristics:

    • Introduces reactivity and often increases polarity.

    • The term ‘R’ group typically refers to the remaining part of the molecule associated with the functional group.

    • Many functional groups enable both intra- and intermolecular interactions such as hydrogen bonds.

    • Common elements in these groups include Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), with some containing Sulfur (S) and Phosphorus (P).

Common Oxygen-Based Functional Groups

  • Functional Group Examples:

    • Hydroxyl–

      • Class: Alcohols and Phenols

      • Structure: ROH

      • Naming: Add ‘-ol’

      • Properties: Acts as a hydrogen bond donor and acceptor.

    • Carbonyl–

      • Aldehydes: RCHO, Naming: Add ‘-al’ (e.g., Methanal).

      • Ketones: RC(=O)R’, Naming: Add ‘-one’ (e.g., Propanone).

      • Properties: Highly electronegative oxygen can act as a hydrogen bond acceptor.

    • Carboxyl–

      • Class: Carboxylic acids

      • Structure: RCOOH, Naming: Add ‘-oic acid’ (e.g., Ethanoic acid).

      • Properties: Two electronegative oxygen atoms, both acting as hydrogen bond donors and acceptors. Can exist as a deprotonated ion (-COO-).

    • Esters– RCOOR’, Properties: Similar to carboxyl but linkage between alcohol and acid.

    • Alkoxy–

      • Class: Ethers

      • Structure: ROR’

      • Naming: List R groups in order of length and insert ‘-oxy’.

Other Important Functional Groups

  • Amino Group

    • Class: Amines (RNH2)

    • Properties: Can form hydrogen bonds, differing in primary, secondary, and tertiary amines.

  • Amides: RCONH2, similar to carboxylic acids but -NH2 replaces -OH.

  • Thiol: RSH, known for forming disulfide bonds critical in protein structures.

  • Thioester: RCOSR, similar to esters with a thiol linkage.

  • Phosphates: RPO4H2, reactively linked with carboxyl groups to form acyl-phosphate groups.

Chemical Reactions

  • Types of Reactions:

    • Heterolytic Reactions: Unequal electron sharing, influenced by the electronegativity of involved atoms.

    • Covalent Bond Formation: Occurs by sharing valence electrons to complete outer electron shells.

    • Bond Breaking:

      • Homolytic: Electron pairs split into separate atoms generating free radicals.

      • Heterolytic: Electrons remain paired with unequal distribution of charge.

Electronegativity and Functional Groups

  • Definition: Electronegativity refers to an atom's ability to attract electrons, affecting the molecule's polar nature.

  • The polarity of bonds in functional groups is crucial for reactivity; for example, carbonyl oxygen gains a partial negative charge, making carbon electrophilic and attracting nucleophiles.

  • Reactions Impacted by Electronegativity: Substitution and addition reactions occur frequently in protein synthesis, DNA replication, and ATP metabolic processes.

Importance of Electronegativity in Reactions

  • Bond Polarity and Reactivity: Allows for complex biochemical encounters and transitions.

  • Example of Acyl Substitution Reactions: Leaving groups are displaced as polar covalent bonds allow new groups to form.

  • Understanding and analyzing these reactions is pivotal for grasping the biochemical processes addressed in subsequent lectures and tutorials.