Case 1: Biochem

Question 1

Role of dietary proteins in burn injury repair

Answer 1

Dietary proteins provide amino acids which are the building blocks for proteins required by the body

Question 2

General structure of an amino acid

Answer 2

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.

Question 3

Major determinant of the folded native structure of proteins

Answer 3

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)

Question 4

What is a ‘native structure’ of a protein

Answer 4

• the form in which the protein exists in an intact cell
• biologically active
• with uniquely folded structure

Question 5

Hydrophobic effect

Answer 5

• 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

Question 6

Bonds that stabilise secondary structure

Answer 6

• noncolavent bonds between the protein backbone (between C=O and -NH)

Question 7

Significance of cyclic amino acids (Proline)

Answer 7

• reduces flexibility about the C-NH bond

- abundant in the collagen helix

Question 8

Amino acid residue

Answer 8

the part of any amino acid that is present when an amino acid is combined in a peptide chain

Question 9

Primary structure of a protein

Answer 9

• defined amino acid sequence
• maintained by covalent peptide bonds
• contains the information required for correct folding of a protein

Question 10

Secondary structure of a protein

Answer 10

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

Question 11

Tertiary structure of a protein

Answer 11

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

Question 12

Quaternary structure of a protein

Answer 12

• spatial arrangement of subunits of a multi-subunit protein.

Question 13

Bonds that are broken by protein denaturation

Answer 13

• non-covalent bonds

Question 14

Structure and function of myoglobin

Answer 14

• structure: single polypeptide chain containing prosthetic group haem
• function: storage of oxygen

Question 15

Function of the polypeptide chain in myoglobin

Answer 15

• protect haem from haem iron from oxidation. Folded structure of polypeptide chain provides haem binding site.

Question 16

Significance of the quaternary structure of haemoglobin

Answer 16

allows for cooperative binding, which satisfies the function if Hb - become fully saturated with O2 in lungs and much less saturated in peripheral tissues.

Question 17

Explain the binding cooperativity of Hb

Answer 17

• 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.

Question 18

Define: allosteric protein

Answer 18

multisubunit proteins which exhibit cooperativity.

Question 19

List the negative effectors of haemoglobin

Answer 19

1. H+
2. BPG
3. CO2

reduce O2 affinity and promote CO2 release.

Question 20

The effects of negative effectors on Hb P50

Answer 20

• P50 = the PO2 at which Hb is 50% saturated with O2

- negative effectors reduce affinity thus increases P50

Question 21

The Bohr effect & its significance

Answer 21

• 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.

Question 22

The effect of CO2 on Hb

Answer 22

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.

Question 23

The effect of 2,3-BPG

Answer 23

• 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

Question 24

Structure of a collagen fibre:

Answer 24

• 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

Question 25

Structure of a tropocollagen molecule

Answer 25

• made up of 3 left-handed helices wound around each other to form a right-handed triple helix
• triple helical structure provides tensile strength to tropocollagen molecule
• tropocollagen stabilised by interchain hydrogen bonds between backbone C=O & NH groups

Question 26

Structure of a collagen microfibril

Answer 26

• a large number of tropocollagen molecules pack side by side to form a single collagen microfibril - added strength
• packing of tropocollagen molecules side-by-side in a staggered way, prevents formation of lines of weakness - further strength
• covalent cross-links linking tropocollagen - further strengthen the microfibril

Question 27

Structure of elastic fibre

Answer 27

• elastin enables elastic fibres to stretch to several times their length and record to original length when force is removed
• rich in non-polar residues -> hydrophobic effect (internalisation of hydrophobic side chains) allows for recoiling of fibre after force is removed
• Lys residues cross-links to limit the extent to which elastic fibres can stretch