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BIOL1024 Fundamentals of Biochemistry > Protein interaction and quaternary structure > Flashcards

Protein interaction and quaternary structure Flashcards

1
Q

insulin biosynthesis process begin

A

single chain formed - pre-proinsulin

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2
Q

insulin biosynthesis in ER

A

A and B peptide form disulphide bonds forming proinsulin

proinsulin kept linkage between A, B, C peptide due to joining chains

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3
Q

insulin biosynthesis in Golgi

A

joined chains are removed = only A and B linkage using disulphide bond = insulin

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4
Q

Denature experiment

A

A and B - form wrong linkage
linkage between A-A or B-B
B with 2 A linked on both sides

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5
Q

protein-protein interaction

A

transient / stable

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6
Q

system biology V Reductionism - including location and time

A

genome - DNA
transcriptome - RNA
proteome - protein
metabolome - metabolites

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7
Q

metabolites

A 
sugar
nucleotide
amino acid
lipid
all go to phenotype or function
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8
Q

reversible protein modification

A

addition of:
small chemical groups - e.g. phosphorylation
complex molecules - e.g. sugar - Paul Skipp
polypeptide - e.g. Ub

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9
Q

small molecules like lysine-acetylation (methylation)

A

for gene expression - able to access DNA

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10
Q

acetylation

A

opens up DNA allowing transcription factors to access strands

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11
Q

lysine side chain - protein on protein

A

used to make isopeptide bonds with carboxyl terminus of Ub

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12
Q

proteins can have prosthetic groups

A

other non-protein molecules can be also conjugated

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13
Q

example of protein having prosthetic groups

A

glycoprotein with prosthetic group of saccharide

example - immunoglobulin - for antibodies

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14
Q

irreversible modification of amino acid

A

e.g. deamidation of Asn/Gln
proteolytic cleavage
partially unfolded intermediates

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15
Q

breaking peptide bond

A

can only be broken by hydrolysis by boiling in 6M acid or alkali

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16
Q

protease can be

A

indiscriminate or sequence specific

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17
Q

trypsin function

A

cuts C-terminals to arginine and lysine - useful in proteomics for mass spectroscopy

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18
Q

protein-protein interaction and quaternary structure

A

proteins form networks and form larger complexes

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19
Q

examples of protein forming networks

A

monomers, dimer, trimer……oligomer, polymer

homomeric/heteromeric

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20
Q

apoptosis

A

caspases cleave after Da.aD (aspartic residue)

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21
Q

homomeric

A

all same subunit

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22
Q

heteromeric

A

different subunits

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23
Q

example of protein-protein interaction

A

Haemoglobin

24
Q

Haemoglobin structure

A

2 a-globin + 2 b-globin + 4 haem

- heterotetramer or dimer of 2 heterodimers

25
Q

zymogens

A

precursors of enzymes - activated in proteolytic cascade after - releases as granules into duodenum

26
Q

microtubule

A

heterodimer - a and b tubulin = MT subunit

27
Q

actin filament formation

A

turning G-actin into F-actin

28
Q

G-actin

A

globular protein

29
Q

F-actin

A

fibrous protein

30
Q

actin (and friends)

A

central binding molecules for many things

e.g. myosin, cell division etc

31
Q

proteins interact via

A

motif or domain

32
Q

motif

A

short, usually primary sequence

33
Q

domain

A

larger, usually structural

34
Q

forces/attraction/bonds used for protein-protein interaction

A

same as observed in tertiary structure

35
Q

example of interaction

A
  • conformational changes to allow a new site of interaction
  • some proteins act as ‘scaffold’ for other to bind onto
  • protein can compete for binding sites
  • protein can have prosthetic groups
36
Q

protein examples of interaction

A

shown how they work and interact

use that knowledge to apply to other interaction

37
Q

conformational changes to allow new site of interaction example

A

PKR

38
Q

PKR

A

kinase - activated when double stranded RNA is present in cell - usually sign of viral infection

39
Q

dsRNA

A

double stranded RNA

40
Q

dsRNA binding to PKR at inhibitory domain

A

changes conformation and allows dimerisation and activation of kinase

41
Q

autophosphorylation of PKR

A

phosphorylates substrate - switch of general translation

inhibits ability of virus replication

42
Q

some protein act as ‘scaffold’ for others to bind onto

A

spatial organisation
colocalisation
scaffold-mediated complex assembly

43
Q

spatial organisation

A

compartmentalisation such as mitochondria

44
Q

colocalisation

A

bind close to membrane

45
Q

scaffold-mediated complex assembly

A

gathering protein - increase efficiency

input - protein phosphorylates/triggers next protein until output

46
Q

protein compete for binding site example

A

regulation of elF2E availability for binding ‘scaffold’

47
Q

when making protein - scaffold protein

type of ‘molecular mimicry’

A

4E binds to another (scaffolding) protein ( in this example, the elF4G)
inhibitory protein - similar sequence at binding site to scaffolding protein

48
Q

to stop protein 4E from binding to inhibitory protein

A

has signalling pathway

kinase phosphorylates inhibitory protein - changes charge and stops el4E from binding to inhibitory and binds to elF4G

49
Q

unwanted protein-protein interaction

A

motif/domain recognition is ‘blind’ to rest of protein

not able to recognise some antigens

50
Q

antibodies - in unwanted protein-protein interaction

A

antibodies coded to recognise foreign antigens can instead cause autoimmune disease

51
Q

example of autoimmune disease caused by unwanted protein-protein interaction

A

multiple sclerosis, Crohn’s, Lupus, Type 1 diabetes

52
Q

example of excessive protein aggregation - genes containing polyglutamine

A

Huntington’s disease

53
Q

genes contains polyglutamine track expansion

A

translation forms gene contain glutamine track expansion = misfolded protein
forming aggregated protein - gain of function

54
Q

example of excessive protein aggregation - genes encode wild type protein sequence

A

Creutzfeldt-Jakob disease

55
Q

genes encode wild type protein sequence

A

form protein conformation 1 protein conformation 2

protein conformation 2 cause aggregated protein - gain of function

BIOL1024 Fundamentals of Biochemistry (25 decks)

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