Week 4 Protein structure

• Structure of proteins:

  • Protein molecules have a 3 dimensional conformation that allows it to fulfil a specific biological function

  A) primary

  B) secondary

  C) tertiary

  D) quaternary

  
• Structure of a peptide bond:

  • has a partial double bond characters
  • means it is quite rigid and nearly planar

  A) d-

  B) d+

  
• Double bonds don't allow free rotation:

  A) 120

  
• Almost all peptide bonds are in the trans configeration, however some are cis

  A) trans

  B) cis

  
• Rotation around bonds connected to the alpha carbon

  A) phi

  B) psi

  C) positive

  D) negative

  
• Secondary structure:

  • refers to the local spatial arrangement of the polypeptide backbone
  • such as alpha helix, beta sheets, turns and loops
  • stabilised by hydrogen bonds (peptide NH and CO groups)
• Alpha helix:

  • coiled structyre that is stabilised by hydrogen bonds between nearby bonds within the helix
  • Side chains point out and are roughly perpendicular with the helical axis
  • schematic views of alpha helices include ribbons (like ferritin) and cylinders (like myoglobin)

  A) carbon

  B) hydrogen

  C) nitrogen

  D) oxygen

  E) side chain

  
• Beta sheets:

  • they are composed of two or more beta strands, which are fully extended
  • beta sheets are stabalised by hydrogen bonds between strands (peptide NH and CO groups)
  • they can be parallel, antiparallel or mixed

  A) parallel

  B) anti parallel

  C) mixed

  
• A protein rich in Beta sheets:

  • arrows in the diagram point in the direction of the carboxyl-terminal end
  • beta sheets may be flat or twisted

  
• Beta turns and Omega loops:

  A) beta turn

  B) omega loop

  
• Tertiary structure of a protein:

  • refers to the overall spatial arrangement of atoms in a protein
  • it is stabilised by interactions between amino acid side chains
  • interacting amino acids aren't necessarily next to each other in the primary sequence

  
• Ionic bonds:

  • a chemical bond between two oppositely charged ions

  A) Glutamate

  B) Histidine

  C) Lysine

  
• Hydrogen bonds:

  • is a bond between a hydrogen and an electronegative atom (N, O)

  
• Hydrophobic forces:

  • a molecules behaviour when exposed to water

  
• Amino acid distribution in a globular protein:

  • water soluble proteins fold into compact structures
  • interior consists mainly hydrophobic amino acids
  • exterior consists of charged and polar amino acids

  A) hydrophobic

  B) polar

  
• Formation of a disulfide bridge:

  • occurs between two cysteine residues
  • can occur within a polypeptide chain or between 2 polypeptide chains

  A) oxidation

  B) reduction

  C) within

  D) between

  
• Quarternary structure:

  • protein composed of multiple polypeptide chains called subunits
  • dimer = two subunits
  • homodimer = 2 identical subunits
  • heterodimer = 2 different subunits

  
• Interactions between protein complexes:

  A) matrix

  B) inner membrane

  C) outer membrane

  D) intermembrane

  
• The amino acid sequence dtetermines the 3 dimentional strcture of a protein:

  A) denaturation

  B) renaturation

  C) removal

  D) addition

  E) inactive

  
• some proteins require assisted folding:

  A) intermediate

  B) native

  C) aggregates

  
• Some proteins need help folding:

  A) unfolded

  B) folded

  C) chaperone