exam 1 lecture 1

• What proteins do


  • Catalysis: Enzymes speed up chemical reactions
  • Defense: Antibodies and complement proteins attack pathogens
  • Movement: Motor and contractile proteins move the cell or molecules within the cell
  • Signaling: Proteins convey signals within and between cells (hormones, receptors, etc.)
  • Structure: Structural proteins define cell shape and comprise body structures
  • Transport: Transport proteins carry materials - Membrane proteins control molecular movement into and out of the cell

  
• Amino acid side chains


  Chemical properties and conformation dictate protein function
• Proteins


  • Conformational flexibilities and interactions with other proteins contribute to their multiple functions
  • Some polypeptides with dissimilar sequences fold into similar 3D structures
  • Homologous proteins evolved from a common ancestor, have similar sequences, structures, and functions, and can be classified into families and superfamilies
• Protein structure and function are key for cell function
• Genome sequencing allows cataloging the proteome and predicting structure and function
• Electrically charged side chains


  Can form ionic and hydrogen bonds
• Polar side chains


  Partial charges can form hydrogen bonds
• Nonpolar side chains


  No charged or electronegative atoms to form hydrogen bonds
• Amino acid side chain properties


  • Electrically charged
  • Polar
  • Nonpolar
• Protein structure has a hierarchical organisation: primary, secondary, tertiary, and quaternary
• Primary structure


  • Amino acid sequence
• Secondary structure


  • Local folding, e.g. alpha helices and beta sheets

  • 60% α-helices and β-sheets

  • remaining: irregular, coils,

  turns and knots
• Tertiary structure


  • Overall 3D conformation, determined by interactions between hydrophilic and hydrophobic residues
• Quaternary structure


  • Assembly of multiple polypeptide chains
• Protein tertiary structures


  • Globular
  • Fibrous
  • Integral membrane
  • Intrinsically disordered

  
• Conformation selection


  Induced fit - protein structure changes to accommodate ligand binding
• Protein domains


  Functional domains exhibit particular activities, structural domains are stable, distinct regions that can act as modules in other proteins
• Quaternary structure


  • Homomeric vs heteromeric subunits
  • Supramolecular complexes can have 10s-100s of polypeptides and be >1 MDa in size
• Varied protein sequences can yield similar structures, as seen in the evolution of heme-binding oxygen-carrying proteins

  
• Protein folding


  1. ATP-dependent molecular chaperones assist folding, refolding, and disassembly

  2. Chaperonins provide folding chambers to allow time and space for proper folding
• Misfolded proteins can form well-organized amyloid fibril aggregates, which are associated with diseases like Alzheimer's and Parkinson's
• Protein function depends on binding to other molecules like ligands, hormones, DNA, and extracellular matrices
• Enzymes


  Accelerate rates of cellular reactions by lowering activation energy and stabilizing transition-state intermediates
• Enzyme resistant


  Characteristic of proteins that misfold and aggregate into amyloid fibrils
• Diseases associated with protein misfolding and amyloid formation


  • Alzheimer's (Tau)
  • Parkinson's
  • Spongiform encephalopathy
  • Prions
• Protein (mis)Folding


  • Misfolding
  • Mutation
  • Inappropriate covalent modifications
  • Chemical/pH stress
  • Heat stress
  • Disrupts function, usually leads to degradation
  • Sometimes, plaques form inside OR outside cells
• Amyloid formation


  1. Cross β-sheet

  2. H-bond into filament

  3. Twist into protofilaments

  4. Thicker amyloid fibrils
• Amyloidoses


  Diseases associated with amyloids; enzyme resistant
• Protein function depends on binding other molecules (ligands)
• Ligands


  • Hormones • receptors
  • Transcription factors • DNA
  • Cell adhesion molecules • ECM matrices
• Enzymes


  • Accelerate rates of cellular reactions by lowering activation energy and stabilizing transition-state intermediates
  • Often use acid-base catalysis mediated by one or more amino acid side chains
  • Metabolic pathway enzymes may be associated as domains of a monomeric protein, subunits of a multimeric protein, or components of a protein complex assembled on a common scaffold
• Enzyme concentration and affinity for its substrate


  Dictate the rate of a reaction
• Catalytic triad


  Related serine proteases have different side-chain specificities in their binding pockets
• Catalytic site


  • Asp-102 interacts with His-57 to activate Ser-195 for nucleophilic attack on the peptide bond to be cleaved
  • Oxyanion hole stabilizes the tetrahedral transition state
  • Arginine side chain (R3) binds the C-terminus of the substrate
  • Side-chain-specificity binding pocket determines which amino acids are preferred at the P1 position of the substrate
• Proteins can be isolated from other cell components on the basis of a variety of physical and chemical properties
• Proteins can be detected and quantified by various assays and specific antibody recognition

  
• Tagging with various types of markers can be used to investigate protein synthesis, location, processing, and stability
• 1. ray crystallography, cryoelectron microscopy, and NMR spectroscopy reveal 3D structures of proteins
• Gel filtration chromatography


  • Separates proteins based on molecular weight
• Ion-exchange chromatography


  • Separates proteins based on charge