Exam 03-01-2018

Front 1

Define gibbs free energy

Back 1

The amount of energy in a system capable of doing work.

Negative = exergonic, spontaneous

Positive = endergonic, nonspontaneous

Front 2

The biochemical standard statens of [H+], [H2O] and [Mg2+]

Back 2

[H+] =10^-7M

[H2O] =55,5M

[Mg2+] =1mM

Vigtig info. De medtages ikke i beregningen af ligevægtskonstanten, K_eq

Front 3

In thermodynamics, What type of system are living organisms and cells?

Back 3

Open system

Hint 3

The exchange both material and energy with the surroundings

Front 4

What is the equation for calculating the equilibrium constant, K_eq?

Back 4

Hint 4

Tænk på en reaktion med produkt og reaktant

Front 5

What is the equation for standard free energy change?

Back 5

Hint 5

Det er den med K_eq.

Front 6

Equation for the free energy change

Back 6

Hint 6

Det er ikke standard gibbs fri energi, men gibs fri energi.

Front 7

How does living cells lower the activation energy?

Back 7

Enzymes

Front 8

How does an endegonic reactions in living cells become a spontaneous process?

Back 8

By coupling the endergonic reactions with a very exergonic reaction.

Ex. Glucose to glucose-6-phosphate coupled with hydrolysis of ATP to ADP and Pi

Hint 8

Front 9

How does K_eq help determining if the coupling of 2 reactions are spontaneous?

Back 9

By multiplying the 2 reactions K_eq.

If the total K_eq increases, then the reaction happens spontaneously

Hint 9

Front 10

The structure of ATP

Back 10

Carrier of energy

Hint 10

Adenosin tri phosphate

Indeholder

3 phosphate, ses på navnet

Adenosin = fructose molekyle med 2 ringe af aminer

Front 11

Structure of NAD+

Back 11

Carrier of electrons

Front 12

The reaction of ATP hydrolysis

Back 12

Front 13

Aerob respiration:

where?

how?

how many ATP pr. mol glucose?

Back 13

Happens in the cytoplasma (glycolysis) and mitochodria (pyruvate oxidation)

Glycolysis --> pyruvate dehydrogenation --> TCA --> ETC --> ATP synthase

30-32 mol ATP pr. mol glucose

Front 14

What is the product of pyruvate in anaerob conditions? (fermentation)

Back 14

produces either:

2 ethanol + 2CO_2

or

2 Lactate

Front 15

Anaerob respiration:

where?

how?

how many ATP pr. mol glucose?

Back 15

Happens only in cytoplasma

From glucose to pyruvate (does not use O_2), and through lactate fermentation produce NAD^+. As for yeast --> ethanol fermentation.

2 mol ATP pr mol glucose

Front 16

Gluconeogenesis:

where in the body?

cost and reqirements?

where in the cell?

Back 16

Happens in the liver, the renal cortex and the small intestine

cost 4 ATP and requires that there is cytoplasmic NADH

Happens in the mitochondria, the endoplamic reticulum and in the cytoplasm

Front 17

the sum reaction of glycolysis

Back 17

Front 18

sum reaction of gluconeogenesis

Back 18

Front 19

How many steps does the hydrolysis of ATP and transfer of phosphorylgroup from ATP to substrat?

Back 19

2 steps.

1. Step is when a phosphoryl group is dissociated from ATP forming ADP.

2. The phosphorylation of the substrate, results in an unstable intermediate. This means that the phosphoryl group would be a good leaving group and therefore dissociate.

The product of the hydrolysis is stable.

Front 20

In the preperatory phase of glycolysis, how many ATP is used?

And how many ATP are produced in the payoff phase of glycolysis?

Back 20

2 ATP are used

4 ATP are made

Front 21

When are energy (ATP) produced?

Back 21

1. When a stable product is produced from an unstable intermediate (free energy < 0)

2. When electrons are transported to reactants with higher affinity. (free energy < 0)

Front 22

What are the 4 fates of glucose in the cell?

Back 22

1. Storage

2. Synthesis of polysacharides

3. Glycolysis to produce ATP and NADH

3. Pentose phosphate pathway to produce ribose 5-phosphate and NADPH

Front 23

What are the 3 fates of pyruvate?

Back 23

1. Oxidation of pyruvate to acetyl CoA - > TCA - > ETC (aerobic conditions)

(anaerobic conditions)

2. Fermentation of pyruvate to lactate to produce NAD+

3. Fermentation of pyruvate to ethanol.

Front 24

In glycolysis why do we phosphorylate the glucose?

Back 24

1. Because the cells membrane does not have phosphate gl. transporter

So the phosphorylated sugar intermediate can not leave the cell.

2. Lowers the activation energy by binding of Pi and enzymes bindingsite (typically Mg2+)

3. High-phosphorylated intermediates donate Pi to ADP to produce ATP

Hint 24

1. tænk på transport af phosphoryleret glucose gennem membranet

2. tænk på den høje aktiverings energi der skal overkommes.

3. villigheden til at donere phosphoryl grupper.

Front 25

which steps in the glycolysis are Substrate Level Phosphorylations?

Back 25

Step 7 and 10

step 7:

conversion of 1,3 bisphosphoglycerate to 3 phosphoglycerate via the enzyme phosphoglycerate kinase

step 10:

conversion of PEP to pyruvate via the enzyme pyruvate kinase

Hint 25

de steder hvor der dannes ATP

Front 26

which steps in the glycolysis uses ATP?

Back 26

Step 1 and 3.

step 1:

conversion of glucose to glucose 6-phosphate via the enzyme hexokinase

step 3:

conversion of fructose 6-phosphate to fructose 1,6-bisphophate via the enzyme phosphofructokinase 1 (PFK1)

Front 27

is the glycolysis the reverse of glyconegenesis?

Back 27

No, even though most of the processes in glycolysis are reversible, 3 reactions are irreversible in the glycolysis.

steps 1, 3 and 10.

in step 1 of gluconeogenesis:

the enzyme used to convert pyruvate to oxaloacetate is pyruvate caboxylase.

step 2.

oxaloacetate converted to PEP via PEP carboxylase

step 9.

from fructose 1,6-bisphosphate to fructose 6-phosphate via fructose 1,6-bisphophatase

step 11.

from glucose 6-phosphate to glucose via the enzyme glucose 6-phophatase

Hint 27

Tænk på de irreversible processer i glycolysen.

step 1, 3 og 10.

Front 28

What is the difference between transketolase and transaldolase?

Back 28

Transketolase:

moves 2 Carbons and utillizes the co-factor TPP (thiamine pyrophosphate)

Transaldolase:

moves 3 carbon no enzymes/co-factor used.

Front 29

which step in the glycolysis produces NADH?

Back 29

step 6:

where glyceraldehyde 3-phosphate is converted to 1,3 bisphosphoglycerate via the enzyme glyceraldehyde 3 phosphate dehydrogenase

Front 30

Which protein/protein complexes and metabolites contribute to electron transport in ETC (electron transport chain)?

Back 30

NADH dehydrogenase (complex 1)

Succinate dehydrogenase (complex 2)

Cytochrome C oxidoreductase (complex 3)

Cytochrome oxidase (complex 4)

Ubiquinone

Ubiquinol

Cytochrome C

NADH

Succinate

Hint 30

Front 31

what is the structure of ubiquinone?

Back 31

oxidized form

Front 32

What is the reaction equation for the convertion of pyruvate to acetyl coA? (pyruvate dehydrogenation)

Back 32

Front 33

what is the name of the enzyme complex responsible for the convertion of pyruvate to acetyl coA? and which 3 enzymes form the enzyme complex?

Back 33

pyruvate dehydrogenase complex

formed by E1 (pyruvate dehydrogenase), E2 (dihydrolipoyl transacetylase) and E3 (dihydropoyl dehydrogenase)

Front 34

Which 5 co-factors contribute to pyruvate dehydrogenation? and what are the functions of these co-factors?

Back 34

TPP = decarboxylates

lipoate=reductive acetylation

coenzyme A =reacts with the dehydrated pyruvate

NAD^+ = electron transporter

FAD = electron transporter

Front 35

What is the net equation for the Citric acid Cycle?

Back 35

Front 36

shortly and precisely decribe what happens in these steps

Back 36

1. emulsification

2. triacylglycerol (TAG) degraded to monoacylglycerol and free fatty acids (FFA)

3. the monoacylglyceroids and FFA are absorbed in the intestinal cells and TAG are restored.

4. chylomicrons (acts as lipid transporter) are incorported in TAG.

5. TAG is transpoted via the lymphatic system and into the blood stream.

6. TAG is hydrolysed via the capillary adipose tissue to 3 FFA and glycerol, which is catalysed by lipoprotein lipase

7. the FFAs are absrobed in the adipocytes and the glycerol is sent to the liver.

8. the 3 FFA are deesterified with glycerol 3-phosphate and converted to TAG. TAG is stored in lipid droplets.

Front 37

how does the ATP synthase work? for F1

Back 37

F1 region:

- responsible for hydrolizing ATP

- subunits alpha and beta make a hexamer with 6 binding sites. three of these are catalytically inactive and bind ADP, while the other three catalyze ATP synthesis

- subunits gamma (central shaft), delta and epsilon are a part of the rotational motor.

- The gamma subunit allows beta to go through conformational changes (beta-ADP, beta-empty, beta-ATP)

- for every 3 protons entering the half-channel P-side and exiting from the half-channel N-side, the "shaft"/gamma rotates 120 degrees.

- for every rotation, the beta bindingsites changes conformation.

Hint 37

Front 38

how does the ATP synthase work? for F0

Back 38

F0 region:- proton enters half-channel P-side- Proton displaces Arg^210 to adjacent subunit c- Arg^210 rotates displacing the proton from Asp-Displaced proton exits on N-side- c10 ring rotates, Arg^210 returns to P-side half-channel- process repeats

Front 39

mention the 8 types of reactions and the enzymes that catalyze the reaction in the citric acid cycle.

Back 39

1) Claisen condensation --> enzyme = citrate synthase

2) dehydration/rehydration --> enzyme = aconitase

3) oxidative decarboxylation -->

enzyme =isocitrate dehydrogenase

4) oxidative decarboxylation --> enzyme = alpha-ketoglutarate dehydrogenase complex

5) substrate level phosphorylation --> enzyme=succinyl-CoA synthetase

6) dehydration --> enzyme = succinate dehydrogenase

7) hydration --> enzyme =fumerase

8) dehydrogenation --> malate dehydrogenase

Hint 39

Front 40

Agents that interfere with oxidative phosphorylation.

which agents inhibits the electron transfer?

Back 40

sodium azide, cyanide and carbon monoxide (inhibits cytochrome oxidase/ complex 4)

Antimycin A (blocks electron transfer from cytochrome b to cytochrome c1)

myxothiazol, retenone, amytal, piercidin A (prevents electron transfer from Fe-S center to ubiquinone)

Front 41

Agents that interfere with oxidative phosphorylation. which agents inhibits the ATP synthase?

Back 41

Aurovertin (inhibits F1)

Oligomycin, Venturicidin (inhibits F0)

DCCD (Blocks proton flow through F0)

Front 42

Agents that interfere with oxidative phosphorylation. which agents uncouples of phosphorylatiob from electron transfer?

Back 42

FCCP, DNP (hydrophobic proton carriers)

Valinomycin (K^+ ionphore)

Front 43

Products of Glycolysis, Pyruvate dehydrogenation and TCA used to calculate the mol of ATP produced during the cellular respiration.

Back 43

NADH = 2,5 ATP, unless its from the glycerol 3 phosphate shuttel, den its 1,5 ATP

FADH_2= 1,5 ATP

Glycolysis:

2 ATP

2 NADH

Pyruvate dehydrogenation:

2 NADH

TCA: 2 rounds

2 ATP

6 NADH

2 FADH_2

Front 44

What is the product of the beta oxidation for one pass?

Back 44

1 FADH2

1 NADH + H+

1 Acetyl-CoA

1 Acyl-CoA which is 2 Carbon shorter

Front 45

shortly explain the 3 steps of activation of fatty acids and transport into the mitochondria.

Back 45

1. fatty acid is activated by Acyl-CoA synthetase to produce fatty acyl-CoA esters. (cytosol)

2. fatty acyl-CoA esters undergoes transeterification, which is catalyzed by carnitine acyl-transferase 1 (CPT1) to produce fatty acyl-carnitine. (in the outer membrane)

the fatty acyl-carnitine would then diffuse across the intermembrane space and enters the matrix through acyl-carnitine/carnitine cotransporter (in the inner mitochondrial membrane).

3. Carnitine acyl-tranferase 2 regenerates fatty acyl-CoA, by dissociating carnitine from the fatty acid. the fatty acyl-CoA would then be released in the matrix and the carnitin can be reused.

Hint 45

the carnitine shuttle

Front 46

Mention the enzymes, products and types of reactions of the four basic steps of the beta oxidation

Back 46

step 1. dehydrogenation catalyzed by the enzyme Acyl-CoA dehydrogenase. the product will be trans- 2 -enoyl-CoA and FADH2. (double bond between beta and alpha Carbon and trans configuration)

step 2. Hydration catalyzed by enoyl-CoA hydratase and forms beta-hydroxy acyl-CoA.

step 3. Degydrogenation catalyzed by beta-hydroxyacyl-CoA dehydrogenase and forms beta-ketoacyl-CoA and NADH + H+.

step 4. cleavage catalyzed by acyl-CoA acetyltransferase (thiolase) forms acetyl-CoA and Acyl-CoA, which is 2 carbon shorter

Important info: The FADH2 and NADH will immediately transfer 2 electrons to the respiratory chain through Electron-transferring flavoprotein (ETF) and NADH dehydrogenase (complex 1 in ETC)

Hint 46

Front 47

shortly explain the 11 processes in the picture

Back 47

1. A low level of blood glucose concentration = release of glucagon. Glucagon (hormone) binds to the receptor in the adipocyte membrane.

2. stimulates adenylyl cyclase via Gprotein and produces cAMP. This activates Cyclic AMP-dependent protein kinase (PKA)

3. PKA phosphorylates the Hormone Sensitive lipase (HSL)

4. PKA also phosphorylates perilipin molecules (the purple on the picture)

5. phosphorylation of perilipin causes dissociation of the protein CGI-58 from perilipin.

CGI-58 recruits adipose triacylglycerol lipase (ATGL) and AGTL becomes active.

6. Active AGTL converts triacylglycerols to diacylglycerols.

7. the phosphorylated perilipin asssociates with the phosphorylated HSL, where it converts diacylglycerols to monoacylglycerols.

8. Monoacylglycerol lipase (MGL) hydrolyzes monoacylglycerol to fatty acid and glycerol

9. Fatty acids leave the adipocyte and are transported in the blood bound serum albumin.

10. Fatty acids are released from serum albumin and enter a myocyte via a specific fatty acid transporter

11. fatty acids go through the betaoxidation, TCA and oxidative phosphorylation to create ATP, which fuels the muscle contraction and other other energy-requiring metabolism in the myocyte.