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BIOL1024 Fundamentals of Biochemistry > Tertiary structure > Flashcards

Tertiary structure Flashcards

1
Q

helix-turn-helix super secondary structure

A

A-T base pair can be recognised by amino acid

H-bonds between A-T at major grooves

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2
Q

coiled coil

A

alpha-keratin form from amphipathic helices

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3
Q

EF hand

A

calcium ligand

helix-turn-loop

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4
Q

tertiary structure

A

folding polypeptide where R-group interact

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5
Q

noncovalent forces/bond

A

hydrophobic interaction
H-bond
VdW and electrostatic

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6
Q

covalent

A

disulphide bonds

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7
Q

disrupting protein structure

A 
heat
pH
ionic
denaturing agent
proteolytic enzymes
UV/oxidative/radiation damage
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8
Q

Disrupting protein structure by heat

A

20-40 degrees

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9
Q

normal intercellular pH

A

7.2 +/- 0.4

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10
Q

ionic strength

A

0.1M KCl

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11
Q

denaturing agents

A 
organic solvent
chaotropic agent (urea, guanidinium hydrochloride)
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12
Q

proteolytic enzyme

A

proteases

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13
Q

Hydrophobic collapse

A

prime driving force for protein folding

- HP cluster of non-polar amino acids

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14
Q

Pi bond interaction - pi-stack/pi-overlap

A
  • aromatic amino acid only

- mixing of clouds of pi e-

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15
Q

how Pi bonds interaction are disrupted

A

by heat

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16
Q

how HP collapse is broken

A

by organic solvent/denaturing agent

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17
Q

H bonds

A
  • involve polar non-charged R group
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18
Q

how H-bonds are broken and exposed

A

by heat, denaturing agents

exposed H-bonds - disrupted by water

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19
Q

Hydrophobic interactions

A

HP collapse

Pi bond interaction

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20
Q

VdW interaction

A

very short range effect

weak electrostatic forces

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21
Q

how VdW interactions are broken

A

by heat, denaturing agent

22
Q

electrostatic bonds

A

ionic interaction - salt bridge

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

23
Q

when electrostatic bonds are in effect

A

anytime unless surrounded by HP interaction

24
Q

zwitterionic form

A

protonation state of R group affected by pH

25
Q

isoelectric point (pl)

A

pH where side chain has not net charge

26
Q

pKa of ionising group

A

pH where 50% ionisation has occurred

27
Q

Henderson Hasselbasch desciption

A

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

28
Q

Henderson Hasselbasch equation

A

HA A- + H+

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

29
Q

charge of protein determined by

A

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

30
Q

salt bridges, ionic bonds

A

made/broken by change in pH

31
Q

result of change in pH for changing electrostatic bonds

A

causes charge of relevant side chains to appear/disappear

32
Q

pH in lysosome and that function

A

4.5 - 5 around

activates activity of lysosomal enzymes

33
Q

changing ionic strength of changing environment

A

also has same effect on lysosomes

34
Q

amino acid use in labs

A

using 6 His
Ni2+ - NTA resin
EDTA

35
Q

use of 6 His

A

to purify protein which can be engineered into gene

36
Q

use of Ni2+ - NTA resin

A

insoluble

cobalt can be used as well

37
Q

use of EDTA

A

chelation

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

38
Q

phosphorylation of hydroxyl groups

A

Ser, Thr, Tyr - important molecular switch

as they have hydroxyl groups

39
Q

phosphorylation effect

A

changes charge of R-group

40
Q

phosphorylation - using aspartate

A

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

41
Q

phosphorylation - using alanine

A

create unswitchable version

therefore kinase can’t add phosphate onto hydroxyl therefore unswitchable

42
Q

Anfinsen experiment on Ribonuclease - native form to fully unfolded

A

add 8M and excess beta-mercaptoethanol

43
Q

disulphide bonds

A

important for extracellular protein

inside cell oxidising potential is low therefore need special enzymes usually taken place in ER

44
Q

example for disulphide bonds

A

cysteine and cysteine - add oxygen to form cystine

add beta-mercaptoethanol to reverse

45
Q

reverse from unfolded to native form on ribonuclease

A

remove urea and beta-ME by dialysis

bubble oxygen = >90% = native form

46
Q

formation of 1% regain activity

A

remove beta-ME and bubble oxygen then dialyse out urea

47
Q

formation of 99% regain activity - native form

A

add trace amount of beta-ME

remove urea and letting bonds form back

48
Q

result of Anfinsen experiment of ribonuclease

A

folded, active form protein has lowest free energy

all info need by protein to fold to this structure is encoded in primary structure

49
Q

in experiment some proteins require

A

protein disulphide isomerase (PDIs)

50
Q

correct conformation achieved by

A

making and breaking disulphide bonds

examples of ‘chaperone’

BIOL1024 Fundamentals of Biochemistry (25 decks)

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