Protein structure and function Flashcards
Decribe primary, secondary, tertiary and quaternary structure
Primary: linear arrangement of amino acid sequence
Secondary: spatial arrangement of polypeptide chain held together by hydrogen bonds between the backbone (alpha helix, beta sheets)
Tertiary: 3-D arrangement of the polypeptide chain, stabilised by interactions between R groups. Forms structural and functional domains
Quaternary structure: interaction of polypeptide chains in a multimeric protein.
Describe the secondary structure of proteins
alpha helix: backbone of the polypeptide forms hydrogen bonds at every 3-4 amino acids, creating a spiral structure with the side chains pointing outward.
beta sheet: consists of laterally packed beta strands. beta strands are short (5-8 residue) fully extended polypeptide segments. Hydrogen bonds occur between the backbone of separate, adjacent beta strands formind a 2D beta pleated sheet. Sheets can be parallel or antiparallel.
Define oxygen saturation
The occupancy of the O2 binding site in a population of molecules.
Describe the biosynthesis of fibrillar collagens
- Procollagen alpha chains are synthesized on RER. Asp-linked oligosaccharides are added to the C-terminal propeptide
- Propeptides associate to form trimers and are covalently linked by disulphide bonds. Selected residues in the Gly-X-Y triplet repeats are covelently modified: Hydroxylation of proline and lysine, some hydroxylysines are glycosylated.
- Modification facilitates stabilisation of triple helices. Chaperone protein Hsp47 binds to helices
- Folded procollagens transported to the Golgi apparatus where it is grouped into smaller bundles
- Chains are secreted and the propeptides at the N and C terminus are removed.
- Trimers are assembled into fibrils and covelently cross-linked
- Staggering of the trimers gives fibrils a striated appearance.
Describe 4 post-translational modifications of collagen
Hydroxylation of proline and lysine (stabilise helix formation)
Isomerisation (lysine to Allysine)
Glycosylation (creates more open structure)
Cross-linking (enbles fibril formation)
Phosphorylation
Describe the main subtypes of collagen
Fibrillar collagen
type 1: bone, skin
type II: cartilage,
type III: walls of arteries, intestine and uterus
Sheet forming collgen:
type IV: basal lamina (kidney)
anchoring collgen:
epidermal junctions
How does the primary and secondary structure of collagen relate to its function?
Primary structure consists of tripeptide repeats. Glycine present at every 3rd residue. Glycine is vvery small and therefore enables helix formation in the presence of ‘bulkier’ amno acid side chains of hydroxyproline and hydroxylysine.
Secondary structure of collagen is a alpha helix. These wind together to form a strong superhelix which gives collagen it’s elastic properties and allows flexibility.
Describe 3 collagen diseases and explain how they arise
Fibrosis: overproduction of collagen produces fibrous tissue in organs.
Ehlers-Danlos syndrome: Mutations in procollagenase enzymes or alpha collagen chains causes defective cross-linking Affects type I and type III collagens. Results in rubbery skin, hypermobility
Osteogenesis imperfecta: (brittle bone disease) Mutation of glycine to bulkier amino acids. Glycine is required at every third position in order for the triple helix to form, and therefore helices are poorly formed and unstable. One defective alpha chain is sufficient to disrupt the whole structure of the molecule. (autosomal dominant)
Scurvy: Vitamin C is a co-factor for the proline hydroxylase enzyme. Lack of Vitamin C means pro-alpha chains are not hydroxylated sufficiently to form stable triple-helical procollagen and it cannot form fibrils. This results in skin, tendons and blood vessels becoming fragile.
Describe the molecular mechanism of co-operative binding
Heme is a prosthetic group made up on an iron atom cound to a protoporphyrin ring. The porhyryn group in deoxy heamoglobin is not planar because the iron atom is too large to fit into the ring. Binding of oxygen to iron rearranges the electrons within the atom and it becomes smaller, moving it into a planar comformation.
This structural change is transmitted to other Hb subunits because the pul moves residues at teh alpha-beta interface. This increases the oxygen affinity of other heme groups and favours the T-R transition.
How is the binding of oxygen to myoglobin related to its structure and function?
Myoglobin is a compact monomeric protein that facilitates oxygen movement in muscles. The binding of oxygen to myoglobin is unregulated, myoglobin is saturated at low partial pressures of oxygen. Myoglobin therefore behaves like an ‘on-off switch’ oxygen is either bound or it isn’t.
How does the binding of oxygen relate to the structure and function of haemoglobin?
Haemoglobin is a heterotetramer composed of two alpha and two beta chains each containing a heme group. This allows each haemoglobin molecule to carry four molecules of oxygen.
The binding of oxygen to haemoglobin is cooperative which means that the binding of one oxygen molecule increases the affinity of haemoglobin chains to bind oxygen. Hb is saturated at high pO2 and tends to lose oxygen at low pO2. This is because the binding of oxygen is regulated allosterically by H and CO2 which lower its affinity for oxygen.
Describe the allosteric regulation of haemoglobin
Hb affinity for oxygen is determined by electrostatic interactions at the alpha-beta interface. DeoxyHb hat 8 more electrostatic interactions than OxyHb.
Binding of oxygen to a Hb chain increases the affinity of Hb by reducing these interactions, which opens up binding sites on other chains in the Hb molecule.
H, CO2 and BPG lower the oxygen affinity of Hb by increasing electrostatic interactions. H+ binds to N-term amino groups on alpha chains, CO2 causes carbamation of Hb which makes N-term groups negatively charged and BPG binds to the centre of the Hb globular structure.
Describe the oxygen dissociation curves
Myoglobin has a low p50 for oxygen. This means that it binds oxygen with high affinity as it 50% saturated at low partial pressures of oxygen.
Foetal Hb has a higher affinity for oxygen than HbA (adult Hb) because it is made of alpha-gamma chains. Foetal pO2 tend to be lower than adults and therefore a higher affinity for oxygen is required to allow diffusion of O2 tot eh foetus across the placenta. Foetal-Hb also has a lower affinity for BPG than HbA which favours oxygen unloading across the placenta
Name five factors which lower the affinity of Hb for oxygen
Increase in temperature
Increase in pCO2
2,3, BPG
low pH (increase in H+)
type of Hb
All shift oxygen dissociation curve to the right
How does carbon monoxide affect the affinity of Hb for oxygen?
Haemoglobin binds with carbon monoxide 200-250 times more readily than with oxygen. The presence of carbon monoxide on one of the 4 haem sites causes the oxygen on the other haem sites to bind with greater affinity. This makes it difficult for the haemoglobin to release oxygen to the tissues and has the effect of shifting the curve to the left (as well as downward, due to direct competitive effects of carbon monoxide).
With an increased level of carbon monoxide, a person can suffer from severe tissue hypoxia while maintaining a normal pO2.
