Case 1: Biochem Flashcards
Role of dietary proteins in burn injury repair
Dietary proteins provide amino acids which are the building blocks for proteins required by the body
General structure of an amino acid
alpha carbon attached to an R(side chain), a carboxyl group, and an amino group. R group for each amino acid is unique, this confers properties to different a.a.’s.
Major determinant of the folded native structure of proteins
amino acid side chains
(amino acids are linked via peptide bonds between alpha carboxyl and alpha amino groups. in this polypeptide chain, the R groups of amino acid residues are free to interact withe each other and the environment)
What is a ‘native structure’ of a protein
- the form in which the protein exists in an intact cell
- biologically active
- with uniquely folded structure
Hydrophobic effect
- An effect whereby a protein folds with non-polar side chains buried in the interior, away from water. Polar groups protrude on the surface of the protein.
- occurs in an aqueous environment and is not due to the attraction of non-polar groups.
- drives the folding of globular proteins in an aqueous environment
Bonds that stabilise secondary structure
- noncolavent bonds between the protein backbone (between C=O and -NH)
Significance of cyclic amino acids (Proline)
- reduces flexibility about the C-NH bond
- abundant in the collagen helix
Amino acid residue
the part of any amino acid that is present when an amino acid is combined in a peptide chain
Primary structure of a protein
- defined amino acid sequence
- maintained by covalent peptide bonds
- contains the information required for correct folding of a protein
Secondary structure of a protein
Local folding of a polypeptide backbone to form regular, repeating structure. Stabilised by H bonds between the backbone, creating rotation around single bonds.
- alpha helix and beta pleated sheets
Tertiary structure of a protein
compact folding of the polypeptide chain that brings into proximity amino acid residues that are distal with respect to the primary structure. (e.g. globular protein)
- stabilised by non covalent bonds (hydrophobic effect, hydrogen bonds, electrostatic interactions.
- some proteins have disulphide bonds formed by cystein
- globular protein - a protein whose polypeptide chain(s) are folded to give the whole molecule a rounded shape
Quaternary structure of a protein
- spatial arrangement of subunits of a multi-subunit protein.
Bonds that are broken by protein denaturation
- non-covalent bonds
Structure and function of myoglobin
- structure: single polypeptide chain containing prosthetic group haem
- function: storage of oxygen
Function of the polypeptide chain in myoglobin
- protect haem from haem iron from oxidation. Folded structure of polypeptide chain provides haem binding site.
Significance of the quaternary structure of haemoglobin
allows for cooperative binding, which satisfies the function if Hb - become fully saturated with O2 in lungs and much less saturated in peripheral tissues.
Explain the binding cooperativity of Hb
- at lungs: binding of O2 at one haem on Hb increases the affinity to O2 at the remaining haemes. This is due to the interaction between Hb subunits.
- at peripheral tissue: release of O2 from one haem increases the tendency for O2 to dissociate from remaining haemes.
Positive cooperativity: between subunits. Affects both binding and dissociation of O2.
Define: allosteric protein
multisubunit proteins which exhibit cooperativity.
List the negative effectors of haemoglobin
- H+
- BPG
- CO2
reduce O2 affinity and promote CO2 release.
The effects of negative effectors on Hb P50
- P50 = the PO2 at which Hb is 50% saturated with O2
- negative effectors reduce affinity thus increases P50
The Bohr effect & its significance
- High [H+] at metabolically active tissues (lactic acids) leads to protonation of some basic groups on HB, which form electrostatic interaction with the anionic groups. This stabilises deoxygenated Hb thus favours the release of O2.
- Low [H+]: oxygenation breaks the electrostatic bonds, H+ dissociates from basic groups of Hb, stabilising the oxygenated Hb.
- significance: enables Hb to offload more O2 to metabolically active tissues which produce H+. These active tissues require more O2 for energy generation.
The effect of CO2 on Hb
CO2 forms carbamates with the N terminal amino groups of Hb, which then form more electrostatic bonds and stabilise decoy-Hb.
- in lungs: reverse occurs. Oxygenation breaks electrostatic bonds. CO2 dissociates from Hb and exhaled.
The effect of 2,3-BPG
- BPG = inside RBC’s regulate long term changes in O2 affinity
- Prolonged hypoxia = increased [BPG]
- effect: decreases O2 affinity thus facilitates O2 release
- Binds to central cavity of Hb tetramer, stabilised by the electrostatic forces between its - charges and + charges of protein functional groups
- low pO2: BPG binding stabilises deoxy Hb and shifted equilibrium torwards O2 dissociation
- high pO2: central cavity narrows and BPG pushed out of cavity
- Hb stripped of all BPG has a high affinity for O2
Structure of a collagen fibre:
- 1 tropocollagen molecule: triple helix
- Many tropocollagen molecules pack to form a collagen microfibril
- many microfibrils form a collagen fibril
- many fibrils pack to form collagen fibre
