protein structure

Question 1

peptide bonds

Answer 1

very stable, cleaved by proteolytic enzymes (proteases or peptidases)
• Partial double-bonds, Flexibility around C atoms not involved in bonds

Question 2

Van der Waals

Answer 2

weak attractive interactions between atoms due to fluctuating electric charges. Only important when 2 macromolecular surfaces fit closely in shape, can also be repulsive at very short distances

Question 3

hydrogen bonds

Answer 3

interaction between dipoles involving hydrogen and an O/N

Question 4

hydrophobic forces

Answer 4

uncharged and non-polar side chains are poorly soluble in water are repelled by water. Hydrophobic side chains tend to form tightly packed cores in the interior of proteins

Question 5

ionic bonds

Answer 5

between fully or partially charged groups

Question 6

disulphide bonds

Answer 6

in extracellular domains of proteins. Conditions can be harsher so extra stability is conferred by covalent bonds between side chains of cysteine residues

Question 7

primary structure

Answer 7

linear sequence of aa linked by peptide bonds, determines its 3D structure

Question 8

secondary structure

Answer 8

alpha helix: H-bonds between each carbonyl group and the H attached to the N which Is 4 aa along the chain. Proline breaks the helix. Beta-sheet: formed by H-bonds between linear regions, cains from 2 proteins or same protein, parallel or anti-parallel, if chain folds back it is called a hairpin loop

Question 9

tertiary structure

Answer 9

3D conformation, more bonds, barrels, bundles, saddle, can change with pH

Question 10

quaternary structure

Answer 10

3D structure composed of multiple subunits, same non-covalent interactions as tertiary structures

Question 11

how do we determine structure?

Answer 11

x-ray diffraction of protein crystals

Question 12

enzymes

Answer 12

Bind to reactants (substrates) and convert them into products then release the products and return their original form, speed up and regulate reactions. Can be used as disease markers and drug targets

Question 13

Haemoglobin and myoglobin

Answer 13

• Porphyrin ring – at the core, holds iron atom so is called heme, iron atom is the site of oxygen bonding
• Temperature, H+ and carbon dioxide affects saturation of haemoglobin by modifying its structure and altering its affinity for oxygen

Question 14

sickle cell anaemia

Answer 14

• Genetic disorder characterised by the formation of hard, sticky, sickle-shaped red blood cells
• Disease is caused by a mutation in haemoglobin
• Adaptation to malaria

Question 15

immunoglobulin (antibodies)

Answer 15

• Produced to bind antigens, typically toxins or proteins on the surface of microbial agents. Targets are labelled for destruction by cells of the immune system of by lysis through the complement system
• Structure – supporting scaffold that displays highly variable loops of complimentary determining regions allows range of reversible bonding affects between antibody and antigen, antigen binding site positioned at tip of supporting structural framework. Arms of antibody can hinge to allow degree of movement
• Antibody/antigen interaction is the close proximity of the antibody CDR regions and the antigen surface, intimate contact allows combination of weak interactions to produce a strong binding surface
• Proportion of antigen bound – epitope
• Bulky amino acid groups can project from the antigen surface