Structures

Question 1

Sperm Whale Myoglobin

Answer 1

alpha helices 
hydrogen bonds buried
hydrophobic pocket binds name
staggered carbon maximise packing and interactions
hydrophobic core drives folding 
his93 coordinates Fe
his64 binds O2

Question 2

Horse Haemoglobin

Answer 2

quaternary, tetramer

Question 3

Lysozyme

Answer 3

degrades sugars in bacterial cell wall
folds making a specificity pocket
recognition slots
Glu35, Asp52 catalyse breakage of glycosidic bond

Question 4

Serine Protease

Answer 4

beta sheet slightly twisted

S195, H57, D102

Question 5

Secondary Structure

Answer 5

H: helix
E: extended, strand
O: other

Question 6

Chou and Fasman

Answer 6

P > 1 secondary structure likely
P(i/a,b,t)/P(i)
hydrophobic => alpha
hydrophobic => beta
nucleation P > 1
extend P 1

Question 7

Antibody

Answer 7

light chain splits
heavy chain below
disulphide bonds
CDR loop recognises antigen

Question 8

Folding

Answer 8

hairpin loop
helix-loop-helix (bind metal)
greek key
rossman fold (beta-alpha-beta)

Question 9

Evolution

Answer 9

point mutation
gene duplication
exon shuffling
alternate splicing

Question 10

Homologous

Answer 10

evolve from similar ancestor

Question 11

Paralogous

Answer 11

related structure, different position between related species

Question 12

Orthologous

Answer 12

related structure, identical position

Question 13

Insulin

Answer 13

stored crystalline
hexameter with 2 x Zn
degrades to 3 x dimers when released

Question 14

Relaxin

Answer 14

similar to insulin (monomer)

relaxes pubic ligaments and cervix

Question 15

Homology

Answer 15

related structures retain secondary structures
core retains topology
peripheral regions change - little affect on function
key structural features regions remain the same

Question 16

Aspartyl Proteases

Answer 16

2 x aspartic acids (1 x -ve, 1 x protonated)

DTG catalytic triad

Question 17

Making a Protein Structure

Answer 17

identify related structures - select templates - align target sequence to template

copy structurally conserved regions - build loops - add side chains - refine

Question 18

Interleukin

Answer 18

chemo mine mediates inflammation
alpha or beta
both function with each other’s receptors
ILRA antagonist, blocks action

Question 19

Super folds

Answer 19

stable

TIM barrel

Question 20

CATH

Answer 20

Class
Architecture 
Topology
Homologous superfamily
Sequence family 
Domain