Lecture 1

• Structural motifs

  • Ring-finger motif, zinc-finger motif
• Folding of proteins

  Aided by chaperones (cell machinery)
• Transcriptional and translational complexes

  • Examples of cellular machines
• Domains in proteins

  Regions of tertiary structure
• Proteins in quaternary structure

  Modular and larger than structural motifs, can be structural or functional
• Post-translational modifications

  • Phosphorylation, Ubiquitination
• Energy requirements

  ATP: High energy phosphate bonds, energy currency of the cell; Energy released from ATP when terminal phosphate bond is broken
• Functions of cellular machines

  Include target recognition, binding, linkers, scaffolds, etc
• Allosteric Regulation mechanisms

  • Ca2+ interactions, The GTPase Switch
• Functions of cellular machines

  Transcription, Translation, Protein folding, Transport, Protein degradation
• Macromolecular complexes

  Multiple different protein components, very large, nano machines visible under electron microscopy
• Units of proteins

  Daltons: Protein is measured in kDa, Protein complexes in MDa; Svedberg (Sv): Rate of sedimentation on a centrifuge, bigger it is → faster, greater Sv
• Structural motifs

  Combinations of secondary structures determined by primary sequence
• Assembly of macromolecular complexes

  Diverse modes of assembly around a core subunit, formation of subcomplexes prior to assembly
• Dimerisation/oligomerisation

  Gives rise to quaternary structures
• Heteromers

  Exist when different proteins come together
• Protein synthesis

  Protein sequences encoded by genes (DNA) are translated from mRNA exported from the nucleus
• Protein structure

  Primary structure → Secondary structure → Structural motifs → partially folded intermediate structure → Tertiary structure → Quaternary structure
• Regulation of cellular machines

  Turn them on and off through post-translational modifications, covalent modifications change protein structure with varied consequences
• Advantages of multi-subunit cellular machines

  Adaptability in substrate recognition, flexibility, diversity in function and regulation
• Allosteric Regulation

  Change in protein structure/function due to non-covalent binding by a ligand
• Internal membranes

  Contain specialised protein machines and associated functions