Lectures 12-15: Glucose metabolism

Question 1

energy containing nutrients broken down by catabolism which are then excreted

Answer 1

bond energy transferred

via cofactors fueling anabolic reactions which take simple precursor molecules and make them into macromolecules

Question 2

metabolism

Answer 2

sum of all chemical reactions in the cell

primarily energy producing - catabolism
primary use energy to build complex structures - anabolism or biosynthesis

everything broken down into acetyl coline - converging

cyclic concentration goes up and down i.e. krebs cycle

diverging - anabolic reactions - complex molecules built up i

Question 3

Entropy (disorder) in a closed system increases

Answer 3

increase entropy in order to gain a more stable state

to maintain cellular organisation must be able to extract useable energy from surroundings and release useless energy

Question 4

when the equilibrium constant is 1 = no net energy

Answer 4

when equilibrium constant is
+1 = negative
1 = 0
-1= positive delta G

Question 5

hydrolysis

Answer 5

spontaneous

highly favourable

Question 6

isomerization

Answer 6

same chemical formula at the beginning and end of the reaction
smaller free energy changes
between enantiomers delta g i 0

Question 7

complete oxidation of reduced compounds

Answer 7

strongly favourable
how chemo-trophs obtain energy
reduced fuel with oxygen is stepwise and controlled

Question 8

delta change depends on

Answer 8

the standard change in free energy

actual concentration of products and reactants

Question 9

spin states

Answer 9

reduced fuels are in singlet spin state = all electrons are paired in electron pairs

molecular oxygen is in the triplet spin state = 2 oxygens are unpaired

direct electron transfer from a singlet reduces species to a triplet oxidising species is quantum mechanicaly forbidden

direct oxidation = combustion of biomolecules doesn’t occur readily

NAD, FAD and transition metal ions act as cofactors to catalyse consecutive single electron transfers needed for oxygen utilisation = need to funnel electrons in single or double pairs away from the singlet state so they can react with the triplet state

Question 10

group transfer reactions

Answer 10

proton - ph

methyl

acyl 2C- biosynthesis of fatty acids

glycosyl more than @C- attachment of sugars

phophoryl ATP- activate metabolites = signal transduction

Question 11

ATP

phosphoryl transfer

Answer 11

donor of the phosphate in biosynthesis of phosphate esters

hydrolysis of ATP is highly favourable under standard conditions

better charge separation in products

better solvation of products - hydroxyl group adding in

resonance stabilisation - drives ATP hydrolysis

ADP is more stable

cellular ATP is high above the equilibrium conc. = potent source of chemical energy

Question 12

NAD and NADP redox cofactors

Answer 12

pyridine nucelotides

can dissociate from enzymes after the reaction

oxidation = hydride ion = 2 protons + 2 electrons from an alcohol transferred to NAD+ = NADH = reduced form
electron later injected into electron transport chain to make a proton gradient

Question 13

FAD

Answer 13

shuttles single electron transfers

permits the fate of oxygen as an ultimate electron acceptor

co factors are tightly bound to proteins

Question 14

fate of glucose

Answer 14

1. stored as glucogen starch or sucrose
2. synthesis of structural polymers = extracellular matrix and cell wall polysaccharides
3. make nucleotides - ribose bisphosphate

4 oxidation via glycolysis = pyruvate

Question 15

important of glucose

Answer 15

goodfuel - high bond energy = delta g

can be stored as glycogen

versatile biochemical precursor -carbon skeleton can be rebuilt into many different amino acids + nucleotide bases

survive on glucose only - human brain

Question 16

glucose entry

Answer 16

glucose transporter in membrane = saturable

glucose kept a 2 millimolar in bloodstream

flows down concentration gradient into cell

Question 17

glycolysis

Answer 17

sugar splitting

make ATP and NADH = more ATP in electron transport chain

6C = 2* 3C pyruvates

5 priming + 5 pay off reactions

3 regulated control enzymes

Question 18

gluconeogenesis

Answer 18

make glucose for export to brain and muscle

pyruvate back to glucose but not exact reverse of glycolysis

3 regulated control enzymes

Question 19

glycolysis

1. the preparatory phase

Answer 19

phosphorylation of glucose using hexokinase = glucose 6 phosphate

1st priming reaction = ATP invested

Phosphohexose isomerase

phosphokinase
1 - second priming reaction

aldolase cleaves 6C into 23C phosphates = glycerldehyde 3phosphate + dihydroxyacetone phosphate

Question 20

payoff phase

Answer 20

ATP + NADH out

inorganic phosphate+ NAD = 2NADH

substrate level phosphorylation 2ADP - 2ATP

second atp forming

Question 21

glycolysis

Answer 21

glucose + 2 NAD = + 2ADP + 2 phosphates = 2 pyruvates
2 NADH
2H+ + 2 ATP

used 1 glucose invest 2 atps and 2 NADs

made
2 pyruvates
4 ATPs = net gain of 2
2 NADH reoxidised in ETC to make ATP

Question 22

3 stages of regulation

Answer 22

stages w a large negative delta G are the best to regulate

in glycolysis hexokinase, fructose 6-phosphate and pyruvate kinase

Question 23

phosphofructokinase

Answer 23

tetramer
binds fructose 6 phosphate = fructose 1,6 phosphate

allosteric regulation - sigmoidal curve = activity is regulated

high AP = activity of enzyme decreased

low ATP conc =
enzyme more sensitive - reactivity higher

Question 24

gluconeogenesis

cannot convert fatty acids to sugars
use acetyl CoA as intermediate then pyruvate and back up to glucose 6P

Answer 24

IN:
2 pyruvate
4ATP
2 GTP
2 NADH 
2 H=
4 water

out :
glucose
4 ADP
2 GDP
6 phosphate
2NAD+

brain n nervous sys only use atp from glucose

when glycogen stores are depleted this is our source of glucose

Question 25

glycolysis vs gluconeogenesis

Answer 25

both thermodynamically favourable regulated to prevent futile cycling which is useless to the cell glycolysis mainly in muscle an brain as require high ATP gluconeo - occurs in liver site 3 reversible reactions shared in both pathways: irreversible reaction of glycolysis must be bypasses in gluconeogenesis ``` glycolysis: hexokinasw phosphofructokinase pyruvate kinase all kinases - changing phosphorylation state of the product ``` ``` gluconeogenesis PEPcarboxykinase puruvate carboxylase fructose 1 bisphosphotase gluce 6 phosphotasease ``` g;uconeogenesis is expensive - more energy to make a glucose than burning one

Question 26

pyruvate fates

Answer 26

yeasts ferment to ethanol lactate in hypoxic or anaerobic condition fermentation by lactate dehydrogenase in contracting muscles or acetyl-CoA citric acid cycle

Question 27

pyruvate 3C to acetate 2C

Answer 27

pyruvate dehydrogenase

Question 28

citric acid/ krebs cycle catabloic process makes GTP an reduced cofactor to yield ATP but important for Anabolic roles reactions tht take pyruvate into

Answer 28

in matrix of mitochondria more ATp generation than glycolysis

Question 29

1. acetyl CoA production

Answer 29

``` pyruvate to acetyl co A oxidative decarboxylation of pyruvate first carbons of glucose are fully oxidised catalysed by the pyruvate dehydrogenase complex found in matrix of mitochondria - requires 5 co enzymes TPP lipllysine prosthetic groups FAD NAD CoA co substrate ``` outL NADH + CO2 + Acetyl-CoA

Question 30

2. Acetyl CoA oxidation 3+4 oxidative decarboxylations = 2 NADH * 5 substrate level phosphorylaition ADP = GTP 6 Dehydrogenation = reduced FADH2 electron carrier 7 hydration 8 dehydration rearrangment of hydrogens= NADH efficient energy storage

Answer 30

1. citrate synthase C_C bond formation 2. aconitase *2 rehydration = isomerisation via dehydration/rehydration large positive delta g = unfavourable reaction so equilibrium is pulled to the right hand side 3 isocitrate dehydrogenase * second oxidative decarboxylation NADH produced oxidation of the alcohol to a ketome transfers hydride 2 electrons to NAD NADP= used as cofactor by cytosolic isozyme highly thermodynamically favourable irrivrsible regulated by product inhibition and ATP 4 alpha-ketoglutarate dehydrogenase complex * 3rd oxidative decarboxylation large negative delta g so regulated 5 succinyl-CoA synthetase succinyl co A had a GDP attached phosphate added to it becomes GTP succinate produced CoA lost substrate level phosphorylation favourable small delta g eq to the right 6 succinate dehydrogenase succinate goes to active site of succinate dehydrogenase FAD - FADh2 electrons removed from succinate go into oxidative phosphorylation pathway delta g is 0 = when fumarate is used eq pulled to the right 7 fumarate water in the state of a hydroxl ion aded by fumarate making temporary carbanion transition state 8 malate dehydrogenase * malate converted back to oxaloacetate for citrate synthase one NADH out large positive delta g = unfavourable [oxaloacetate] low pulling reaction forward for 1 turn of cycle = 3 NADH + 1 FADH2 + 1 GTP later = ATP

Question 31

why is pyruvate dehydrogenase complex (made up of pyruvate de hydrogenase E1 + dihydrolipoyl transactylase and dihydrolipoli dehydrogenase E3) efficient multisubunit swinging aim cofactor binding substrae channelling intermediates never leave enzyme surface

Answer 31

1. short distance between catalytic sites allows channeling of substrate from one catalytic site to another 2. channeling minimizes side reactions 3 regulation of activity of one subunit affects the entire complex you only need to modify one of them to modify all of them regulated my phosphorylation

Question 32

citrate synthase - Allosterically controlled enzyme rate imiting step regulated by {oAA] and product inhibition MM would be sigmoidal

Answer 32

changes conformation once binds oxaloacetate open conformation = no binding site for acetyl CoA closed conformation = binding of oxaloacetate creates binding site = induced fit avoid unnecessary hydrolysis of thioester

Question 33

regulation of citric acid cycle

Answer 33

``` enzymes that are reuglated PDH citrate synthase IDH and aKDH = sigmoidal MM curve ``` activated by substrate availablity inhibity by product accumulation NADH and ATP affect all regulated enzymes in cycle inhibitor NADH and ATP activators NAD+ and AMp

Question 34

regulation of citric acid cycle

Answer 34

``` enzymes that are regulated PDH citrate synthase IDH and aKDH = sigmoidal MM curve ``` activated by substrate availability inhibity by product accumulation NADH and ATP affect all regulated enzymes in cycle inhibitor NADH and ATP activators NAD+ and AMp

Question 35

3. Electron transfer + oxidative phophorylation

Answer 35

proton motive force built up across inner membrane =synthesis of atp protons flow back through from inter membrane space into a matrix of the mitochondria electrons from reduced cofactors NADH and FADh2are passed to proteins in respiratory chain oxygen final electron acceptor = water energy of oxidation by flow of protons own the electrochemical gradient used to phosphorylate ADP = ATP energy released by electron transport used to transport protons against electrochemical gradient outer membrane of mitochondria porous permeable to metabolites inter membrane space similar to cytosol high [proton] =low pH inner membrane large surface area due to cristae convolutions location of ETC complexes matrix location of krebs cycle lipid/acid metbaolism low [h+] electrons taken from matrix into inter membrane space protons pumped through by complex 1 and 3 and 4 complex 2 passed though series of electron carriers into inter membrane space and meets oxygen in complex 4

Question 36

each complex contains multiple redox centers

Answer 36

``` 1. flavin mononucleotiode (FMN) or flavin ADEnine (FAD) initial electron acceptors for complax 1 n 2 carry 2 e by tranferring 1 at a time 2. iron-sulfur cluster carry 1 co ordinated by cysteines in the protein 3 coenzyme ubiquinone carry 2 - proton is added so 2 OH groups added ubiquinol reduced result 2 cytochromes a b or c carry 1 e ``` 1. NADH dehydrogenase succinate dehydrogenase ubiquinon cytochrome c

Question 37

COMPLEX 1 proton pump

Answer 37

transfer or. 2 electron from NADH to ubiquinone carrier that can carry 2 per NADH 4 protons from matirx (N) into intermembrane space (P) conenzyme Q picks up 2 protons transported by proton wires =reduced ubiquinone = only soluble in the membrane 2 electrons from NAD+ passed down and meet protons make QH2

Question 38

complex 2 | succinate dehydrogenase

Answer 38

delta g 0 2 electrons stripped off of succinate transferred to FADH2 one at a time via iron sulfur centers in ubiquinone added to protons = QH2 doesn't transport protons reduce [proton] in matrix

Question 39

complex 3 | buiquionen:cytochrome C oxidoreductase

Answer 39

shunts electrons from ubiquinol onto cytochrome and cytochrome moves it onto final complex into inter membrane space moving electrons used 3 electrons from QH2 to reduce t molecules of cytochrome c contains iron sulfur clusters and haem grops Q cycle causes 4 additional protons transported to IMS

Question 40

complex 4

Answer 40

cytochrome released into inter membrane space hydrophiic bump into complex 4 cytochrome oxidase 4 electrons used to reduce one oxygen molecule to 2 waters 4 protons picked up from matrix in this process 4 additional protons passed from matrix to inter membrane space electrons injected via a series of coppor centres to produce water oxygen reduced 1 at time = 2 waters polar but uncharged diffuse out of cell =maintain hypertonic sate huge positive change in intermambrane space made up of protons ATP synthase part of respiratome complex electron transport sets up a proton motive force FoF1 ATP synthase has amembrane binding portion in inner membrane Fo =and head group in matrix protons flow through and spin inner spindle in head at high speed by protons flowing in and back into matrix to meet OH groups f1 soluble in matric making ATP Fo intergral membrane complex tramsports protons back to matrix dissipating the proton gradient energy transferred to F1 to catalyse phosphorylation of ADP ``` hexamer arranged in 3 alpha beta dimers arranged in 3 conformations open = empty loose = binding to ADP and pi tight = catalyses ATP formation and binds product ``` proton translocation causes a rotation of the Fo subunit and the central shaft gamma = conformational change by the gamme subunit rotating inside within all the 3 alpha beta pairs promotes condensation of ADP into ATP

Question 41

binding change model

Answer 41

alpha and beta subunits from dimer release and ATP molecule the gamma spindle pushes ATP off ADP and PI come in to bind and spindle moves to next position particular position inside head required pushing against the beta conformation ATP is churned off ADP + Pi bound state ATP form ATP exclusion from binding site