Tertiary structure

Question 1

helix-turn-helix super secondary structure

Answer 1

A-T base pair can be recognised by amino acid

H-bonds between A-T at major grooves

Question 2

coiled coil

Answer 2

alpha-keratin form from amphipathic helices

Question 3

EF hand

Answer 3

calcium ligand

helix-turn-loop

Question 4

tertiary structure

Answer 4

folding polypeptide where R-group interact

Question 5

noncovalent forces/bond

Answer 5

hydrophobic interaction
H-bond
VdW and electrostatic

Question 6

covalent

Answer 6

disulphide bonds

Question 7

disrupting protein structure

Answer 7

heat
pH
ionic
denaturing agent
proteolytic enzymes
UV/oxidative/radiation damage

Question 8

Disrupting protein structure by heat

Answer 8

20-40 degrees

Question 9

normal intercellular pH

Answer 9

7.2 +/- 0.4

Question 10

ionic strength

Answer 10

0.1M KCl

Question 11

denaturing agents

Answer 11

organic solvent
chaotropic agent (urea, guanidinium hydrochloride)

Question 12

proteolytic enzyme

Answer 12

proteases

Question 13

Hydrophobic collapse

Answer 13

prime driving force for protein folding

- HP cluster of non-polar amino acids

Question 14

Pi bond interaction - pi-stack/pi-overlap

Answer 14

• aromatic amino acid only

- mixing of clouds of pi e-

Question 15

how Pi bonds interaction are disrupted

Answer 15

by heat

Question 16

how HP collapse is broken

Answer 16

by organic solvent/denaturing agent

Question 17

H bonds

Answer 17

• involve polar non-charged R group

Question 18

how H-bonds are broken and exposed

Answer 18

by heat, denaturing agents

exposed H-bonds - disrupted by water

Question 19

Hydrophobic interactions

Answer 19

HP collapse

Pi bond interaction

Question 20

VdW interaction

Answer 20

very short range effect

weak electrostatic forces

Question 21

how VdW interactions are broken

Answer 21

by heat, denaturing agent

Question 22

electrostatic bonds

Answer 22

ionic interaction - salt bridge

between charged residues - acidic and basic, cysteine and tyrosine(ionisable)

Question 23

when electrostatic bonds are in effect

Answer 23

anytime unless surrounded by HP interaction

Question 24

zwitterionic form

Answer 24

protonation state of R group affected by pH

Question 25

isoelectric point (pl)

Answer 25

pH where side chain has not net charge

Question 26

pKa of ionising group

Answer 26

pH where 50% ionisation has occurred

Question 27

Henderson Hasselbasch desciption

Answer 27

relationship between pH, pKa and extent of ionisation of weak acid

Question 28

Henderson Hasselbasch equation

Answer 28

HA A- + H+ | pH = pKa +log([A-]/[HA])

Question 29

charge of protein determined by

Answer 29

pH number of each amino acid type of amino acid with ionisable sidechain

Question 30

salt bridges, ionic bonds

Answer 30

made/broken by change in pH

Question 31

result of change in pH for changing electrostatic bonds

Answer 31

causes charge of relevant side chains to appear/disappear

Question 32

pH in lysosome and that function

Answer 32

4.5 - 5 around | activates activity of lysosomal enzymes

Question 33

changing ionic strength of changing environment

Answer 33

also has same effect on lysosomes

Question 34

amino acid use in labs

Answer 34

using 6 His Ni2+ - NTA resin EDTA

Question 35

use of 6 His

Answer 35

to purify protein which can be engineered into gene

Question 36

use of Ni2+ - NTA resin

Answer 36

insoluble | cobalt can be used as well

Question 37

use of EDTA

Answer 37

chelation | Elute by EDTA but also competition or low pH (His becomes protonated)

Question 38

phosphorylation of hydroxyl groups

Answer 38

Ser, Thr, Tyr - important molecular switch | as they have hydroxyl groups

Question 39

phosphorylation effect

Answer 39

changes charge of R-group

Question 40

phosphorylation - using aspartate

Answer 40

has similar size and charge to Ser | therefore able to mimic switch permanently so protein kinase can't be used and can't be phosphorylated

Question 41

phosphorylation - using alanine

Answer 41

create unswitchable version | therefore kinase can't add phosphate onto hydroxyl therefore unswitchable

Question 42

Anfinsen experiment on Ribonuclease - native form to fully unfolded

Answer 42

add 8M and excess beta-mercaptoethanol

Question 43

disulphide bonds

Answer 43

important for extracellular protein | inside cell oxidising potential is low therefore need special enzymes usually taken place in ER

Question 44

example for disulphide bonds

Answer 44

cysteine and cysteine - add oxygen to form cystine | add beta-mercaptoethanol to reverse

Question 45

reverse from unfolded to native form on ribonuclease

Answer 45

remove urea and beta-ME by dialysis | bubble oxygen = >90% = native form

Question 46

formation of 1% regain activity

Answer 46

remove beta-ME and bubble oxygen then dialyse out urea

Question 47

formation of 99% regain activity - native form

Answer 47

add trace amount of beta-ME | remove urea and letting bonds form back

Question 48

result of Anfinsen experiment of ribonuclease

Answer 48

folded, active form protein has lowest free energy | all info need by protein to fold to this structure is encoded in primary structure

Question 49

in experiment some proteins require

Answer 49

protein disulphide isomerase (PDIs)

Question 50

correct conformation achieved by

Answer 50

making and breaking disulphide bonds | examples of 'chaperone'