Structure of proteins 2

• Describe tertiary structure


  • The 3D folding of secondary structure
  • Hydrophobic residues are buried within the structure and hydrophillic structures are exposed outwards to the aqueous environment
• What is meant by domains of proteins?


  • Many proteins are organised into domains
  • each domain contributes a specific function to the overall protein
  • Different proteins may share similar domain structures
• What can connect alpha helix's and beta sheets?


  Loops/bends connect regions of alpha helix and beta sheet so that the poly peptide can fold into a globular domain
• What bonds can stabilise a tertiary structure?

  • Disulphide bonds
  • Hydrogen bonds
  • Ionic interactions
  • Van der waals interactions
  • Hydrophobic interactions
• Describe disulphide bonds


  • The SH groups of two neighbouring cysteine residues form a covalent S-S bond
• Describe quarternary structure


  • The association of more than on polypeptide
  • Each peptide chain is called a subunit and the complex can be designated as an oligomeric protein
  • Subunits can be identical or different
  • Disulphide bonds often stabilise oligomeric structures
• Describe the structure and function of haemoglobin


  • Carries oxygen in red blood cells (erythrocytes)
  • A symmetrical assembly of two different subunits - 2 alpha globin and 2 beta chains
  • Each of the polypeptide chains contains a haem molecule, which binds oxygen for transport to tissues
• Describe the structure and function of Haem molecules


  • porphyrin ring with coordinated Fe atom - binds oxygen for transport to tissues
  • Each haem molecule is held in place by hydrogen bonds from histidine F8 and the bound oxygen molecule stabilised by histidine E7
• What structural change occurs to the haem molecule after oxygen binding?


  It causes a change to the ring structure
• How does oxygen binding to the haem molecule influence haemoglobin?


  It influences the structure of haemoglobin and the binding of further oxygen molecules
• What is the shape of the haem in the deoxygenated form of the blood cell?


  The haem is domed or non-planar
• What is the shape of the haem in the oxygenated form of the red blood cell?


  The haem is planar
• What happens to the histidine that hydrogen bonds to the haem molecule upon oxygen binding?


  It changes position, causing major structural changes in the globin subunit
• What is the effect of the subtle conformation change in the globin subunit after oxygen binding?


  It causes major structural realignments elsewhere in the molecule
• What is the result of the structural realignments caused by oxygen binding?


  There is a dramatic increase in the binding affinity for subsequent oxygen molecules
• What is the sigmoidal oxygen binding curve


  Demonstrates cooperative oxygen binding

  • affinity of the first oxygen molecule is low but binding of subsequent oxygen molecules is then increased
  • due to changes in the protein structure after the first binding of the oxygen molecule
• What is the biological significance of the sigmoidal oxygen binding curve?


  • Relatively small changes in oxygen concentration result in large changes in the interaction of haemoglobin with oxygen
  • Equates to tight oxygen binding in the lungs and subsequent release in the tissues where oxygen concentration is low
• What causes sickle cell anaemia?


  • Single amino acid change at position 6 in the beta chain of haemoglobin
  • turns hydrophillic glutamic acid to hydrophobic valine
  • this causes the sickling of erythrocytes due to clustering of mutated haemoglobin that forms stiff fibres (change in surface chemistry of the protein)
  • Reduces their ability to carry oxygen
• What effect does pH and CO2 concentration have on haemoglobin?


  Bohr effect - when the pH of the blood affects the O2 binding to haemoglobin

  • O2 binding occurs with higher affinity at high pH (lung) and lower affinity at low pH (peripheral tissues)
  • loading O2 is easier in the lung and unloading occurs much faster where O2 is needed
  • CO2 (acidic) builds up during exercise - lowers blood pH, facilitates faster oxygen delivery
• What is the structure and function of foetal haemoglobin?


  Different quarternary structure

  • Has two alpha subunits and two gamma subunits
  • Lower O2% by the time the blood reaches the placenta so needs to bind with greater affinity than normal haemoglobin
• Can a foetus have sickle cell anaemia?


  No - they do not have a beta chain so they are unaffected by sickle cell disease
• What is collagen?


  • Protein that helps bind cells together to form tissues
  • Assembles in long, extremely strong fibres
  • The chief protein in bone, tendon and skin
  • constitutes 25% of the total protein mass in the body
• Describe the structure of collagen


  • Tropocollagen is the building block of collagen fibre
  • consists of 3 polypeptide chains with a left handed twist wound together in a right handed supercoil
• Describe the role glycine plays in the structure of tropocollagen


  • Glycine - crucial for the formation of tropocollagen triple helix
  • Has a small side chain (one hydrogen) that allows tight turns
  • The small side chian allows close packing of subunits
  • There are three amino acid residues per turn
• Describe the role proline plays in the structure of tropocollagen


  • Vital for the structure
  • imposes a left hand twist in the helix that provides the main stabilising force of this unusual protein structure
  • Some prolines become hydroxylated to form hydroxyproline
  • forms strong hydrogen bonds that help to stabilise the triple helix
• How do the tropocollagen subunits form?


  • individual protein chains come together - form triple helices
  • This forms a molecule known as procollagen - enzyme called procollagen peptidase that cleaves of the loose, non - tightly packed ends
  • leaves behind the tightly packed sub unit called tropocollagen
• Describe the formation of the collagen fibre


  • Through a model called the quarter-stagger model
  • called this because the adjacent subunits are about a quarter of the way along from each other - stronger and more stable
  • Cross linked together through lysine covalent cross links - links between the lysine side chains
  • Lysine gets deaminated by an enzyme called lysyl oxidase to form aldehyde derivative (allysine)
  • when two of these derivatives come together they become cross linked which stabilises the tropocollagen subunits within the collagen
• What can cause the tropocollagen subunits to not pack together properly?


  Genetic mutations

  • mutation in the gene that codes for one of the collagen subunits leading to a glycine being replaced by a cysteine residue at one point in the chain
  • means the subunits cannot pack together properly - creates a knock on effect on collagen fibre formation

  Form of brittle bone disease - osteogenesis imperfecta
• What illnesses can be due to problems in the formation of tropocollagen?


  Scurvy;

  • symptoms
  • dry skin, gum disorders
  • cause
  • lack of proline hydroxylation (Vitamin C)

  Ehlers-Danloss syndrome

  • symptoms
  • Loose skin, hypermobile joints
  • Cause
  • Lack of procollagen peptidase or lysyl oxidase
• How is strength built in to all levels of collagen fibre production?

  Close packing of sub units

  • Glycine every 3rd residue

  Opposing twists of subunits and super helix

  • high proline content

  Hydrogen bonding

  • Hydroxyproline

  Cross - linking

  • lysine- derived aldehydes