tertiary structure

• how do secondary structures connect and fold to form tertiary structures?

  Connect - through loops and bends which are also part of secondary structure

  Fold - through non-covalent as well as covalent forces (not present in all proteins - present when there's disulphide bridges)
• where are loops(bends) and turns found?

  found on protein surfaces and controls the size and shape
• what are loops?

  contains stretch of hydrophilic residues so found on surfaces of proteins. used to connect alpha-helices and beta-sheets together or two of the same together

  usually no regular repetitive structure
• what are turns?

  same as loops but less than 5 residues and can be better defined than a loop - connects secondary structures together and hold tertiary structure together

  most common are B-turns
• what words are used when talking about structure complexity and what do they mean?

  Motif - typical arrangement >two secondary structure elements, e.g. when two 2º structures come together

  Domain - contains motifs that can fold to give stable self-contained tertiary structural unit

  Subunit - may combine many domains
• example of motifs:

  
• most of the time loops just hold the secondary structure together but sometimes they can be used to stabilise the tertiary structure and occasionally the loops do contribute to a function

  e.g. (fourth motif) - loop can accommodate a calcium ion which has a positive charge and the Asp-R groups have a negative charge so it has affinity for divalent ions. (An atom, with a valency of two, which thus can form two covalent bonds)
• complexes of >1 polypeptide chains non-covalently bind in precise ratios and with a precise 3D
• label this:

  A) domain

  B) subunit

  C) quaternary

  D) subunits

  
• what is a homomultimetric protein?

  where the subunits are identical in the protein (exactly the same just in different orientation)
• what is a heteromultimetric protein?

  a protein composed of subunits that are different in sequence and structure
• what are the forces that hold the territory structure together?

  • covalent
  • electrostatic ionic dipole-dipole
  • hydrogen bonds
  • hydrophobic bonding
  • dispersion (Van der Waals) forces
• describe covalent bonds in holding tertiary structure:?

  • strongest side chain interaction - lots of energy associated with it
  • side chain of cysteine forms covalent disulphide bridge
  • Cysteine forms disulphide bonds easily via the thiol group through a process called oxidation
  • it's not present in all proteins
  • 167 kJ/mol

  
• how do the electrostatic ionic + dipole-dipole bonding occur?

  • two oppositely charged molecules attract (can be stronger in non-polar parts of the protein)
• what equation defines the energy of interaction in an electrostatic ionic + dipole-dipole bond?

  A high dielectric constant = E value becomes smaller and so energy interaction is low

  Smaller the distance = the stronger the force

  A) distance

  B) dielectric constant

  C) negative

  
• what solvents have high dielectric constants?

  polar solvents have very high ones like water
• what solvent has a low dielectric constant?

  organic/non-polar - so in membranes there's a low dielectric constant due to the fatty acids
• why are h-bonds important inside proteins?

  they stabilise things a lot easier - a lot of them = interactions are very strong

  3-7 Kcal/mol stabilisation per h-bond
• in tertiary structure - the h-bonds help stabilise the specific arrangement of amino acid residues in different parts of the protein contributing to the overall shape and stability
• what equation can relate to the hydrophobic bonding in proteins?

  Gibbs free energy

  A) enthalpy

  B) entropy

  
• A system is stable if ΔG is negative - as negative as possible

  ΔH needs to be negative and ΔS to be positive so an increase in entropy is desirable
• what is entropy?

  Entropy is a measure of the disorder or randomness in a system. (dynamic exchange)
• hydrophobic bonding - the hydrophobic amino acid side chains tend to cluster together in the interior of the protein to avoid water and present minimum surface area to water. this minimises the loss of energy so ΔS stays quite favourable
• whats the hydrophobic effect?

  • water molecules form a structured network around hydrophobic groups due to hydrogen bonding, however the structuring of water when in a non-polar solvent is energetically unfavourable because it disrupts the randomness and flexibility of water = loss in entropy
  • and so hydrophobic groups tend to cluster together to minimise water exposure, allowing the system to gain entropy as the water molecules ate free to move more randomly and regain some of the lost entropy
• the protein adopts a folded conformation because it represents a lower free energy state compared to the unfolded state - a lower free energy (Gibbs) state = more stable
• dispersion forces are reversible and happen all the time - they are weak but there are lots of them in a whole protein so strong all together
• how are dispersion forces formed?

  • electronic charge in an atom is not evenly distributed all the time and so there's temporary fluctuations in electron density creating temporary dipoles - these are dynamic and constantly changing
  • one dipole induces a dipole to neighbouring/nearby atom and creates a chain effect
• strengths of forces

  A) glu and lys

  B) no direction

  C) weak

  D) S-S

  E) strong

  F) weak

  G) hydrogen

  H) ionic

  
• forming of a tertiary conformation:

  • these are in equilibrium
  • all the polar side chains point towards the water - helps solubilise the protein in water + maximises the entropy as much as possible by having the hydrophobic groups inside
  • water binding to the polar sides exposed to water to form hydration shell surrounding the protein

  
• the main driving force for protein folding in aqueous solution, is the increased entropy of the water molecules when hydrophobic groups bury inside.
• comparisons of fibrous proteins and globular proteins...?

  Fibrous

  • long fibre sheets
  • mechanically strong
  • insoluble in water
  • mainly structural role
  • largely one type of 2º structure

  Globular

  • spherical shape
  • quite delicate
  • soluble
  • diverse role - catalyse, storage, immune defense
  • usually both 2º structures
  • ferritin and haemoglobin
• describe the properties of myoglobin...

  • non allosteric - has only one tertiary structure
  • found in skeletal muscle + is the O2 storage protein
  • small monomeric globular protein - 153 amino acids
  • has a haem prosthetic group where O2 binds
  • 78% of alpha helices linked by turns and no beta sheets
  • folded tertiary structure = hydrophobic residues compacted inside and hydrophilic R groups mainly outside

  
• which amino acid is critical in binding site?

  Histidines
• how many His residues does a haem have near?

  two His residues - each axial to the Fe inside the protein
• the Fe ion has 6 coordination bonds - 4 taken by N atoms of haem, 1 by His and leaving one for functional reasons

  A) proximal

  B) distal

  C) O2

  
• whats the proximal histidine?

  • this is directly coordinated to the iron group in the heme group
  • its primary role is to help stabilise the iron atom in its reduced (Fe2+) state, facilitating the binding of oxygen to the iron
• what is the distal histidine?

  • a His residue not apart of the haemoglobin protein but is located near the heme group
  • the distal histidine forms a hydrogen bond with the oxygen molecule, helping to position the O2 in a way that facilitates its binding to the iron
  • it also helps prevent the oxidation of the iron from ferrous (Fe2+) to ferric (Fe3+) states
• why is it important that the distal His prevents the oxidation of the iron from ferrous to ferric?

  only the ferrous state is capable of binding oxygen reversibly
• what occurs in the heme group when O2 binds?

  • when binds it forms a reversible coordination bond
  • it induces a conformational change in the iron (becomes a bit smaller) and it moves into the plane of the heme, and the entire heme group undergoes a more planar, relaxed structure
  • the distal His helps stabilise the oxygen and in turn stabilise the structure
• how does the iron become smaller when O2 binds?

  Electron density changes around the Fe due to the partial electron transfer to the oxygen and so make sit a bit smaller so it can fit in