Cellular metabolism (Shore)

Question 1

triacylglycerol (TAG) mobilisation from adipose by…

Answer 1

glucagon
adrenaline
cortisol
producing 3 FFA, 1 glycerol

Question 2

FA activation

Answer 2

linked to CoA prior to oxidation in cytoplasm
acyl CoA synthetase allows rapid hydrolysis of pyrophosphate to form a thioester bond which is increased by substrate conc
this is an irreversible initiation step

Question 3

mitochondrial shuttle

Answer 3

shuttle is required because acyl CoA is too large to move across the membrane

acyl-CoA and carnitine via CPT-I is converted to CoASH to acyl-carnitine which moves across the membrane and uses the CAT transporter to allow acyl-carnitine in a carnitine out and then acyl-carnitine can be converted back into CoASH and using CPT-II it can be converted back into carnitine and acyl-CoA which can enter the beta-oxidation pathway

Question 4

unsaturated FAs, types of enzymes required

Answer 4

reductase to reduce the double bond
isomerase for reductase enzyme to work

Question 5

what do you need to deal with propionyl CoA
what vitamin coenzyme does methylmalonyl CoA mutase use? dealing with beta-oxidation for unsaturated FAs

Answer 5

enzymes including propionyl CoA carboxylase(carboxylation), methlmalonyl CoA epimerase (isomerisation), methylmalonyl CoA mutase and TCA which allows succinyl CoA to enter the Krebs cycle

vitamin b12

Question 6

what are ketone bodies used for?
when do ketone bodies rise?
what can and can’t produce glucose from?
uses of ketones?

Answer 6

alternate energy source when glucose is scarce (fasting) because they are water soluble can pass the BBB
animals cannot produce glucose from FFA and the link reaction is irreversible and you cannot make glucose from acetyl CoA but you can from pyruvate
some cell use ketones over glucose such as the heart and adrenal medulla

Question 7

what is the mechanism for fasting or diabetes when using FAs in heart, muscle and in the BBB

Answer 7

FAs taken up by the liver
liver breakdown FAs to make ketone bodies
ketone bodies are exported to other tissues to be converted back into acetyl CoA - this is really important for tissues such as the brain because the brain cannot use FAs themselves

Question 8

beta-hydroxybutyrate dehydrogenase

Answer 8

produces three FAs, acetone is spontaneously produced, all produced from acetoacetyl CoA
reduction is acetoacetate
ration acetate:butyrate
dependent on [NADH+H+] and [NAD] in mitochondria

Question 9

FA synthesis - transport of Acetyl CoA

Answer 9

cytoplasm starting with acetyl CoA
reverse of beta oxidation
can’t use same transporter mechansism to transport acetyl CoA, different to beta oxidation
oxaloacetate to produce citrate with Acetyl CoA out of mitochondria ad converted back into oxaloacetate by ATP and CoA to acetyl CoA ADP+Pi, malate is then converted to pyruvate from NAP+ to NADPH to move the pyruvate into the cell again
this shuttle moves acetyl-coA from mitochondrial matrix to cytoplasm

Question 10

FA synthesis

Answer 10

2 carbon to make 3 carbon
using acetyl CoA carboxylase
committed step coupled to ATP to ADP
this has a regulatory point where adrenaline and glucagon will inactivate the enzyme, whereas insulin will activate the enzyme this is a phosphorylation mechanism for regulation
malonyl CoA and acetyl CoA to produce malonyl ACP and acetyl ACP using enzymes
attaches to carrier protein and is covalently linked to short carbon chains
then the four steps of synthesis
condense 2 carbon and 3 carbon to lose a CO2 which uses condensation
then beta-ketoacyl ACP reductase is used to reduce using NADH (NADH is a reducing agent) and D isomer is formed
then dehydrogenation using 3-hydroxyacyl ACP dehydratase to make a double bond to produce a saturated FA
then another reduction using enoyl ACP reductase to produce butyryl ACP (4C)
then cycle continues to add each cycle 2C, but only goes to 16C but uses enzymes to go further

Question 11

transportation of lipids

Answer 11

FAs from adipose are transported to various tissues bound to serum albumin
phospholipid monolayer with triglycerols in the centre
triglycerides are transported as:
chylomicrons
VLDL
LDL
HDL

Question 12

ubiquitin and what three enzymes? and how does the AA impact the half life of the protein

Answer 12

attached to proteins
marks for degradation

actovating
conjugating
protein ligase
N terminal rule so the AA impact the half life of the protein

Question 13

protein metabolism

Answer 13

breaking down of protein - tagging using ubiquitin
deamination of AA - removal of N
urea cycle - urea production
alanine metabolism - gluconeogenesis
AA synthesis - N fixation

Question 14

cyclin destruction boxes and PEST sequences

Answer 14

short conserved AA sequence which signals the degradation via the ubiquitin- proteasome pathway which is vital for cell cycle regulation

sequences rich in proline, glutamic acid, serine and threonine AAs and this makes it have a short half life but rapid turnover for signalling for protein degradation

Question 15

26S proteasome

Answer 15

19S - recognition
20S - protease

Question 16

AA removal

Answer 16

major site is the liver
the amino group enters the urea cycle and the carbon skeleton enters the TCA cycle
alpha AA produces an alpha ketoacid
alpha AA to glutamate to NADH and NH4+ to then enter the urea cycle because the NH4+ produced is toxic so urea is produced

Question 17

aminotransferases/transaminases

Answer 17

cause the transfer of alpha AA to alpha ketogluterate
examples include aspartate transaminases and alanine transaminase
all require pyridoxal phosphate
reversible synthesis

Question 18

glutamate dehydrogenase

Answer 18

oxidative deamination - nitrogen taken off glutamate to turn it into ammonia and produce alpha-ketoglutarate so that it can be recycled
essentially liver (mitochondria) specific
equilibrium close to 1 in the liver

Question 19

describe the glucose alanine cycle

Answer 19

glycogen in the muscle cell and converted to glucose then converted to pyruvate
the pyruvate has the addition of NH4+ from branched chain AA to produce alanine and carbon skeletons for cellular respiration
alanine is transported from the muscle cell to the liver and produces glutamate where NH4+ can be removed and produces urea and then pyruvate is produced from the splitting of alanine to produce glucose which can then be moved back across to the muscle cell

Question 20

urea cycle

Answer 20

join NH3 to HCO3- to make carbamoyl phosphate which required 2 ATP
the joining of ornithine by anhydride bond formation forms citrulline
this all occurs in the mitochondria and then citrulline is transported outside the mitochondria to the cytoplasm
citrulline is attached to aspartate to produce arginosuccinate which is a condensation reaction this requires energy
argininosuccinase splits the molecule and fumarate and arginine is produced
hydrolysis occurs so ornithine and urea is produced
then several methods but one can be to make malate and then oxaloacetate from fumarate and then using aspartate transaminase to produce aspartate

Question 21

ammoniotelic organisms

Answer 21

fresh water fish which do not do the urea cycle

Question 22

entry points of AA

Answer 22

they can enter at different points of the Krebs cycle, dependent on the carbon skeleton
they are connected to the Kreb’s cycle whether that is via glycolysis but their fate is often in the Kreb’s cycle

Question 23

AA synthesis

Answer 23

N fixation
assimilation of NH4+ using glutamate dehydrogenase to produce glutamate (and glutamine which requires ATP) (requires formation of Schiff base)
six pathways for synthesis of AA which starts with different carbon skeletons

Question 24

N fixation

Answer 24

requires lots of ATP (16)
nitrogenase complex by mitochondria
8 high energy electrons
uses reductase and nitrogenase
process is strongly inhibited by oxygen - needs anaerobic environment

Question 25

link reaction

Answer 25

irreversible pyruvate dehydrogenase and this needs cofactors such as: catalytic cofactors - thiamine pyrophosphate (TPP) and lipoic acid stoichiometric cofactors - CoA and NAD+ there are different subunits for pyruvate dehydrogenase 1 - decarboxylation of pyruvate 2 - oxidation to release energy by forming thioester bond 3 - group transfer - acetyl group (acetylation) which provides energy when the thioester bond is broken as acetyl CoA is produced 4 - oxidation of dihydrolipoamide back to lipoamide, this has to occur before further CoA can be formed from pyruvate, electrons transferred to FAD then to NAD+ overall produce CO2, NADH and acetyl CoA

Question 26

regulation of the link reaction

Answer 26

under adenylate control: ADP, ATP and NAD can undergo covalent modification so phosphorylation will turn it off high ATP turns it off low ATP turns it off

Question 27

mercury poisoning

Answer 27

binds to pyruvate dehydrogenase (E3) inhibits the enzyme hatters used mercury nitrite causing neurological symptoms sulfhydryl treatment

Question 28

beriberi (alcoholics)

Answer 28

B1 deficiency (thiamine) neurological and cardiovascular symptoms raised blood pyruvate levels nervous systems relies on glucose for energy

Question 29

citric acid cycle (Krebs)

Answer 29

1 - C2 (acetyl CoA) + C4 (oxaloacetate) to produce citrate 2 - isomerisation, dehydration then hydration aconitase to rearrange hydroxyl 3 - dehydrogenase oxidises (reduction and decarboxylation) to produce alpha-ketoglutarate with NADH + H+ and CO2 regulatory point 1 in the cycle, this enzyme is regulated (isocitrate dehydrogenase) using allosteric regulation NOT covalent, this is the first enzyme to generate high energy electron, regulation based on levels of ADP,ATP and NADH to make it go faster or slower 4 - decarboxylation and oxidation using redox reaction and a group transfer to produce succinyl CoA regulatory point 2 uses second enzyme to generate high energy electron using alpha-ketogluterate dehydrogenase to down regulate succinate CoA, NADH and ATP 5 - succinyl CoA synthetase used to break high energy thioester bond from succinyl CoA and uses nucleoside diphosphokinase 6,7,8 - oxidation, hydration and oxidation to reform oxaloacetate and then the cycle can continue

Question 30

succinate dehydrogenase

Answer 30

hydrogen acceptor is FAD linked to electron transport chain

Question 31

fumerase

Answer 31

addition of H+ and OH- removal of double bond fumerate --> malate

Question 32

malate dehydrogenase

Answer 32

positive delta G in Krebs cycle doesn't matter if it is positive because as long as it is linked to other reactions that are more negative to make up for this

Question 33

mitochondria structure properties

Answer 33

outer - permeable inner - impermeable, cristae, transport such as shuttles or transporters

Question 34

NADH movement methods

Answer 34

method 1: glycerol 3-phosphate shuttle predominates in muscle to aid fight or flight system because this process is fast takes high energy electrons and shuttling them into Coenzyme Q think 4 potatoes and a mushroom method 2: malate and aspartate shuttle, this is slower than the first mech

Question 35

ATP-ADP translocase

Answer 35

another mechanism transporter which can flip backwards and forwards ADP in and ATP out note that ATP wants to move to the more positive side of the transporter which produces a concentration gradient - causes a problem when more ATP gets moved onto the positive side causing a charge difference and this uses a lot of energy (25%)

Question 36

which of the transporters are proton pumps?

Answer 36

1,3,4 pumping protons into the intermembrane space

Question 37

what are the names of proton pumps 1,3,4 and their function

Answer 37

1 - NADH-CoQ Oxidoreductase - redox reaction NADH oxidised and reduces CoQ uses the energy to pump protons this step is skipped if you use the muscular skeletal way also called NADH dehydrogenase also contains FMN which only accepts one electron at a time and 6-7 iron centres to facilitate redox reactions due to variable oxidation states moves 4H+ 3 - CoQ-Cytochrome c Oxidoeductase - oxidises CoQ by taking electrons and gives cytochrome C cytochrome c can hold one electron, losely bound to inner membrane water soluble cytochromes contain haem proteins carrier electrons to complex IV 2H+ 4 - Cytochrome c Oxidase - oxidises cytochrome c by taking electrons 4H+ sequence of events where the electrons travel through the subunits through these complexes the electrons get passed to oxygen as the last electron acceptor

Question 38

coenzyme Q

Answer 38

lipid based moves freely within mitochondrial inner membrane

Question 39

complex II

Answer 39

succinate-coenzyme Q oxidoreductase contains succinate dehydrogenase to link to Krebs cycle FAD - covalently bound 3x iron sulphur clusters mutations cause variety of disorders - individually rare but collectively common, most mutations in this complex because it is more survivable due to less electrons being put into complex II it completes the succinate fumerate part of the Krebs cycle

Question 40

what is the issue of skipping complex I in OxPhos?

Answer 40

you can use II to III to complex IV but less H+ are pumped into the matrix so when you use FADH2 pathway, only 1.5 mol of energy is produced

Question 41

ROS

Answer 41

partial oxidation there can be leakage produces harmful and reactive chemicals which can be potentially destructive superoxide dismutase and catalase examples

Question 42

give some inhibition of pathways

Answer 42

NADH-CoQ Oxidoreductase can be inhibited (rotenone) (complex 1 inhibited) cytochrome c oxidase - cyanide ferric form of cyt a3 (Fe3+) so cannot use oxygen without ATP carbon monoxide ferrous form of cyt a3 (Fe2+)

Question 43

ATP synthase structure and function

Answer 43

F0 is in the membrane F1 is in the matrix the H+ enters the subunit a from intermembrane space, then transferred into subunit c to where there is a chemiosmotic gradient and force c unit to rotate and spit the proton out of the subunit a again to deposit into the matrix aspartic acid unit inside to attract the protons inside due to its negative charge gamma unit rotates inside the head unit and then head unit is held in place and does not move not a circular shape the proteins change shape into either open, lose or tight shape - in the open state ATP and ADP+Pi can move into it in the loose state - they can't move out in the tight state - orientated to bond together to form ATP

Question 44

control of oxidative phosphorylation

Answer 44

governed by ADP the less ATP and more ADP, the faster ATP synthase works the faster that ATP synthase works, the faster that everything else works Le Chatelier's principle can up regulate and down regulate and this has an effect on the Krebs cycle too electron transport is couples to ATP production in oxidative phosphorylation - a example where they are uncoupled is white adipocyte and brown adipocyte allows the protons to go through this membrane without generating ATP so instead heat is produced