Protein interaction and quaternary structure

Question 1

insulin biosynthesis process begin

Answer 1

single chain formed - pre-proinsulin

Question 2

insulin biosynthesis in ER

Answer 2

A and B peptide form disulphide bonds forming proinsulin

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

Question 3

insulin biosynthesis in Golgi

Answer 3

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

Question 4

Denature experiment

Answer 4

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

Question 5

protein-protein interaction

Answer 5

transient / stable

Question 6

system biology V Reductionism - including location and time

Answer 6

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

Question 7

metabolites

Answer 7

sugar
nucleotide
amino acid
lipid
all go to phenotype or function

Question 8

reversible protein modification

Answer 8

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

Question 9

small molecules like lysine-acetylation (methylation)

Answer 9

for gene expression - able to access DNA

Question 10

acetylation

Answer 10

opens up DNA allowing transcription factors to access strands

Question 11

lysine side chain - protein on protein

Answer 11

used to make isopeptide bonds with carboxyl terminus of Ub

Question 12

proteins can have prosthetic groups

Answer 12

other non-protein molecules can be also conjugated

Question 13

example of protein having prosthetic groups

Answer 13

glycoprotein with prosthetic group of saccharide

example - immunoglobulin - for antibodies

Question 14

irreversible modification of amino acid

Answer 14

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

Question 15

breaking peptide bond

Answer 15

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

Question 16

protease can be

Answer 16

indiscriminate or sequence specific

Question 17

trypsin function

Answer 17

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

Question 18

protein-protein interaction and quaternary structure

Answer 18

proteins form networks and form larger complexes

Question 19

examples of protein forming networks

Answer 19

monomers, dimer, trimer……oligomer, polymer

homomeric/heteromeric

Question 20

apoptosis

Answer 20

caspases cleave after Da.aD (aspartic residue)

Question 21

homomeric

Answer 21

all same subunit

Question 22

heteromeric

Answer 22

different subunits

Question 23

example of protein-protein interaction

Answer 23

Haemoglobin

Question 24

Haemoglobin structure

Answer 24

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

- heterotetramer or dimer of 2 heterodimers

Question 25

zymogens

Answer 25

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

Question 26

microtubule

Answer 26

heterodimer - a and b tubulin = MT subunit

Question 27

actin filament formation

Answer 27

turning G-actin into F-actin

Question 28

G-actin

Answer 28

globular protein

Question 29

F-actin

Answer 29

fibrous protein

Question 30

actin (and friends)

Answer 30

central binding molecules for many things | e.g. myosin, cell division etc

Question 31

proteins interact via

Answer 31

motif or domain

Question 32

motif

Answer 32

short, usually primary sequence

Question 33

domain

Answer 33

larger, usually structural

Question 34

forces/attraction/bonds used for protein-protein interaction

Answer 34

same as observed in tertiary structure

Question 35

example of interaction

Answer 35

- 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

Question 36

protein examples of interaction

Answer 36

shown how they work and interact | use that knowledge to apply to other interaction

Question 37

conformational changes to allow new site of interaction example

Answer 37

PKR

Question 38

PKR

Answer 38

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

Question 39

dsRNA

Answer 39

double stranded RNA

Question 40

dsRNA binding to PKR at inhibitory domain

Answer 40

changes conformation and allows dimerisation and activation of kinase

Question 41

autophosphorylation of PKR

Answer 41

phosphorylates substrate - switch of general translation | inhibits ability of virus replication

Question 42

some protein act as 'scaffold' for others to bind onto

Answer 42

spatial organisation colocalisation scaffold-mediated complex assembly

Question 43

spatial organisation

Answer 43

compartmentalisation such as mitochondria

Question 44

colocalisation

Answer 44

bind close to membrane

Question 45

scaffold-mediated complex assembly

Answer 45

gathering protein - increase efficiency | input - protein phosphorylates/triggers next protein until output

Question 46

protein compete for binding site example

Answer 46

regulation of elF2E availability for binding 'scaffold'

Question 47

when making protein - scaffold protein | type of 'molecular mimicry'

Answer 47

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

Question 48

to stop protein 4E from binding to inhibitory protein

Answer 48

has signalling pathway | kinase phosphorylates inhibitory protein - changes charge and stops el4E from binding to inhibitory and binds to elF4G

Question 49

unwanted protein-protein interaction

Answer 49

motif/domain recognition is 'blind' to rest of protein | not able to recognise some antigens

Question 50

antibodies - in unwanted protein-protein interaction

Answer 50

antibodies coded to recognise foreign antigens can instead cause autoimmune disease

Question 51

example of autoimmune disease caused by unwanted protein-protein interaction

Answer 51

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

Question 52

example of excessive protein aggregation - genes containing polyglutamine

Answer 52

Huntington's disease

Question 53

genes contains polyglutamine track expansion

Answer 53

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

Question 54

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

Answer 54

Creutzfeldt-Jakob disease

Question 55

genes encode wild type protein sequence

Answer 55

form protein conformation 1 protein conformation 2 | protein conformation 2 cause aggregated protein - gain of function