lecture 4

Question 1

steps of glycogen breakdown

Answer 1

broken down by phosphorylase to glucose-1-p to glucose-6-p to pyruvate

Question 2

steps of production of glycogen

Answer 2

UDP-glucose to glycogen by glycogen synthase
OR
glucose to g-6-p to g-1-p to glycogen by phosophorylase

Question 3

what is the role of glycogen phosphorylase in muscle

Answer 3

to provide ATP for muscle contraction

it is activated when ATP is in short supply, a muscle contracts and in a critical situation

Question 4

what is generated by glycogen breakdown for glycolysis

Answer 4

g-6-p

Question 5

how is glycogen phosphorylase allosterically regulated

Answer 5

glycogen phosphorlyase is activated by AMP
activation by amp is antagonised by atp and g-6-p
amp, atp and g6p dont bind the same site
allosteric regulation due to non covalent binding of a small molecule that binds to a site distinct from the active site
g6p is derived from the breakdown of glycogen and so is atp
g6p and atp are both classical feedback inhibitors of glycogen breakdown

Question 6

what is the significance of phosphorylase activation by amp

Answer 6

amp is produced in many enzymatic reactions
major source is catalysed by adenylate kinase
it is a reversible reaction that uses very little free energy and it maintained close to equilibrium in most cells
if adp:atp ratio rises 2 fold, amp:atp rises 4 fold - effects of amp are antagonised by atp, phosphorylase is activated by increased amp:atp - a signal of low cellular energy status
glycogen is broken down to replenish atp when it is depleted

Question 7

what does allosteric regulation maintain

Answer 7

homeostasis

Question 8

how is allosteric mechanisms switched off

Answer 8

reverse the on function

constrained by the equilibrium constant for association:dissociation reaction

Question 9

what are molecular switch mechanisms needed for

Answer 9

to cause a large change in signal output in response to a small change in signal input (large increase of AMP is needed to go from off to on)
molecular switched on and off pathways are different and usually involve covalent mods of proteins

Question 10

adv of allosteric regulation

Answer 10

ligand binding site due to simple non covalent interaction = no enzyme is required
no energy directly consumed by association and dissociation of ligand

Question 11

disadv of allosteric regulation

Answer 11

large changes in ligand conc required to achieve large effects
allosteric reg better for homeostasis than for making changes

Question 12

adv of covalent modifications

Answer 12

interconversion reactions have high energy, must be catalysed by enzymes
for protein kinase reactions, equilibrium is driven by high cellular ratio of atp:adp
for protein phosphate reactions, equilibrium will always lie in favour of dephosphorylation - it is driven by high cellular water conc
small adjustments in relative activities of kinae and phosphate enzymes allow achievement of any desired ratio of protein:phosphoprotein from 0 to 1
protein phosphorylation is therefore good for switching cells from one state to another

Question 13

disadv of covalent modifications

Answer 13

price paid for control of atp is consumed in the phosphorylation cycle

Question 14

2 forms of phosphorylase

how are they two types found

Answer 14

b - allosterically activated by amp
a - doesnt require amp
a - phosphorylated at a single serine residue near n terminus
b - in dephosphorylated form

Question 15

covalent mods of glycogen phosphorylase

Answer 15

phosphorylation is catalysed by a protein kinase ‘phosphorylase kinase’ which is activated by low calcium conc
muscle contractions triggered when stimulation of motor nerves trigger calcium release from sarcoplasmic reticulum of cell
glycogen breakdown is coupled with muscle contraction

Question 16

covalent mods of phosphorylase kinase

Answer 16

phosphorylase kinase is phosphorylated by cyclic AMP - dependent protein kinase, increasing its maximal activity and calcium sensitivity
cAMP increased in the muscle by hormone adrenaline is released during exercise or stress
more rapid and complete conversion of phosphorylase to amp independent ‘a’ when an organism is under stress
hormonal mechanism superimposes on the nervous mechanis, while both over ride allosteric mechanism

Question 17

g protein switch mechanism

Answer 17

conformational change in gtp binding or g protein
a signal activates the gtp/gdp exchange factor
causes a switch of g protein to active gtp bound conformation
active g protein binds and activates downstream effector protein such as cAMP
in absence of continuing stimulation, g protein reverts back to gdp inactive form
gtp hydrolysis is catalysed by g protein and promoted by gtpase activator protein
on and off are different so molecular switch mechanism criteria is fulfilled

Question 18

how is protein phosphorylation a central mechanism

Answer 18

protein kinases often exist in sequences in which one kinase phosphorylates and activates another
as each kinases acts catalytically the signal is amplified
cascades often mediate effects of extracellular signalling molecules or first messengers
kinase casscades often converge and diverge from signalling networks
responses to extra and intra cellular signals can be integrated
dephosphorylation by protein phosphates may also be regulated

Question 19

other types of covalent modification

Answer 19

phosphorylation, ubiquitination, acetylation (all reversible

Question 20

what type of covalent mods are irreversible

Answer 20

those paused by pathogenic bacteria
bacteria causing cholera and pertussis produce protein toxins that enter the host cells and catalyse adp ribosylation of host proteins
cholera is acquired by drinking infected water - its toxin modifies a g protein that controls cAMP production in cells lining airways, causes fluid secretion and severe coughing spreading the infection back into the environment
toxins are v potent as the act catalytically and because host cells have no enzyme to reverse ADP ridosylation

Question 21

blood clotting switch mechanism

Answer 21

reversible switch mechanisms require energy and therefore need the presence of active donors of the modifying group such as atp or nad
outside cells active donors are not present so irreversible modifications are used instead
blood clotting uses cascade of proteinases that activate each other by proteolysis
each clotting factor cleaves an inactive precursor off of its downstream target and activates it
extrinsic clotting pathways triggered when factor 7 forms a complex with tissue factors released from the damaged cells
fibrinogen is soluble but fibrin is insoluble and it aggregates to start the blood clot
proteolysis is irreversible and once used up new clotting factors must be synthesised