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Semester 1- MTM > Metabolism and its Control > Flashcards

Metabolism and its Control Flashcards

1
Q

what is metabolism?

A

Chemical processes that occur within a living organism in order to maintain life.

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2
Q

what is a metabolic pathway?

A

A metabolic pathway starts with a specific metabolite and ends with a product. The first molecule is converted into the last by a chain of enzymatically catalysed reactions. E.g.
Glycolysis: Glucose –> Acetyl-CoA
TCA (Krebs) Cycle: Acetyl-CoA –> CO2

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3
Q

what is a catabolic pathway?

A

when a complex molecule is BROKEN down to a smaller one and energy is RELEASED

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4
Q

what is an anabolic pathway?

A

complex molecule is BUILT from simple one which requires energy in the form of ATP

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5
Q

define oxidation

A

acquisition of oxygen, or loss of electrons, or loss of hydrogen (OIL RIG)

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6
Q

define reduction

A

Loss of oxygen, or gain of electrons, or gain of hydrogen (OIL RIG)

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7
Q

what are the 7 different important metabolic processes?

A

Hydrolysis: Adding water to break apart a molecule
Dehydration: Loss of water
Phosphorylation: Addition a phosphate group
Dephosphorylation: Removal of a phosphate group
Carboxylation: addition of a CO2 molecule
Decarboxylation: removal of a CO2 molecule
Ligation reaction: Joining of two molecules

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8
Q

what is ATP and what is its structure?

A

Adenosine triphosphate – formed from 3 phosphates, ribose sugar, & adenine base

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9
Q

where does ATP store energy?

A

The ATP molecule stores energy in 2 phosphoanhydride bonds
released via hydrolysis of bond.

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10
Q

how much energy does hydrolysis of ATP create?

A

Hydrolysis at physiological pH releases 7.3 kcal

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11
Q

what are the 2 ways in which ATP can be formed?

A

1) substrate-level phosphorylation- doesn’t require oxygen
2) oxidative phosphorylation- requires oxygen

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12
Q

what happens to ATP when its left in room temp for too long?

A

ATP will slowly release inorganic phosphate and be converted to ADP and eventually AMP

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13
Q

what is the equation for respiration?
i.e how much of each product is formed?

A

C6H12O6 + 6O2 –> 6CO2 + 6H2O + 31ATP

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14
Q

what are the 4 different stages in the production of ATP?

A

Glycolysis
Oxidative decarboxylation (Link reaction) TCA cycle (Krebs cycle)
Electron transport chain (oxidative phosphorylation)

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15
Q

describe the process of glycolysis

A

Glucose is primed with 2 phosphorylation reactions & one isomerisation reaction to form fructose-1,6-bisphosphate
fructose-1,6-bisphosphate split to form 2x GA-3-P
2x GA-3-P undergoes dehydrogenation and phosphorylation (catalysed by an enzyme).
2 x NAD coenzymes accept the removed hydrogens forming 2 x NADH (reduced NAD)
The resulting product 2 x 1,3-BGA then undergoes dephosphorylation twice forming 2x pyruvate and 4x ATP molecules.

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16
Q

what are the overall products produced in glycolysis?

A

Glucose –> 2 x pyruvate
2 ADP –> 2 x ATP (net yield of 2 x ATP and 2 x NADH bc 2 ATP molecules were used but 4 were made)
2 NAD –> 2 NADH

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17
Q

where does glycolysis occur?

A

in the cytosol

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18
Q

what do kinase enzymes do in glycolysis?

A

Kinase enzymes transfer a phosphate to a molecule – this creates a high energy phosphate bond

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19
Q

what 2 phases is glycolysis split into?

A

Priming
Splitting

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20
Q

what is priming?

A

ATP is used up in this phase
break down ATP to phosphorylate glucose
then phosphorylate fructose-6 phosphate to form fructose-1,6-bisphosphate

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21
Q

what is splitting?

A

4 ATP molecules are produced during this phase

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22
Q

when would lactate levels rise in the body?

A

exercising skeletal muscle –> increased lactate therefore muscle pain

coronary arteries blocked by atherosclerosis –> insufficient O2 supply to cardiomyocytes leading to increased lactate therefore angina pectoris (chest pains)

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23
Q

what needs to be regenerated in order for glycolysis to continue?

A

NAD+

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24
Q

how is NAD+ regenerated in aerobic and anaerobic respiration?

A

In aerobic respiration this is done using oxygen
In anaerobic respiration this is done in another way
- Lactate fermentation
- Alcoholic fermentation

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25
Q

what happens during lactate fermentation?

A

1) glycolysis –> pyruvate: acts as a hydrogen acceptor taking the hydrogen from reduced NAD, catalysed by the enzyme lactate dehydrogenase.

2) The pyruvate is converted to lactate (lactic acid) and NAD is regenerated.
- used to keep glycolysis going so a small quantity of ATP is still synthesised.

3) Lactic acid is converted back into glucose in the liver (gluconeogenesis) but oxygen is needed to complete this process.
^^ This is the reason for the oxygen debt (and the need to breathe heavily) after exercise.

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26
Q

what happens during alcoholic fermentation?

A

Alcoholic fermentation is non-reversible.

1) Pyruvate (produced by glycolysis) is first converted to ethanal (acetaldehyde), catalysed by the enzyme pyruvate decarboxylase. 1 x CO2 is produced as well.

2) Ethanal can then accept a hydrogen atom from reduced NAD (catalysed by Alcohol dehydrogenases),becoming ethanol.

3) The regenerated NAD can then continue to act as a coenzyme and glycolysis can continue.

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27
Q

what is the cori cycle?

A

a metabolic pathway in which lactate, produced by anaerobic glycolysis in muscles, is transported to the liver and converted to glucose, which then returns to the muscles and is converted back to lactate.

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28
Q

what do most cells have in their PM?

A

Almost all cells have high levels of pyruvate & lactate transporters in their plasma membranes

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29
Q

how does the liver form glucose from lactate?

A

1) The lactate is first converted into pyruvate
2) Pyruvate is then converted into Glucose 6-phophate (gluconeogenesis)
3) Glucose 6-phospahte is then converted into glucose

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30
Q

what is gluconeogenesis?

A

synthesis of glucose from pyruvate
reverse of glycolysis

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31
Q

what enzymes are used in gluconeogenesis?

A

phosphofructokinase
fructose-1,6-bisphosphatase

control whether the glycolysis or gluconeogenesis pathway is followed

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32
Q

how is glucose produced from pyruvate during gluconeogenesis?

A

1) phosphofructokinase converts fructose-6-phosphate into fructose 1-6 bisphosphate to then follow glycolysis and produce pyruvate

2) fructose-1,6-bisphosphatase converts fructose 1-6 bisphosphate into fructose 6 phosphate to then follow gluconeogenesis and produce glucose.

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33
Q

what happens to phosphofructokinase and fructose-1,6-bisphosphatase at high ATP concentrations?

A

at high ATP conc phosphofructokinase is inhibited & fructose-1,6-bisphosphatase is activated –> gluconeogenesis occurs

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34
Q

what is the cost energy of gluconeogenesis?

A

2 pyruvates + 4ATP + 2GTP + 2NADH are required to produce 1 molecule of glucose

35
Q

what is pyruvate decarboxylation and where does it occur?

A

link reaction
occurs in the mitochondria
links glycolysis and Krebs
produces Acetyl CoA from pyruvate

36
Q

what enzyme converts pyruvate to Acetyl CoA?

A

pyruvate dehydrogenase complex
(PDH complex)

37
Q

what is the PDH complex made up of?

A

made up of three enzymes –
pyruvate dehydrogenase
dihydrolipoyl transacetylase
dihydrolipoyl dehydrogenase

38
Q

what is the structure of the PDH complex?

A

A: Decarboxylation of pyruvate to form an Acetyl Group
B: Acetyl group is combined with coenzyme A forming Acetly CoA
C: In the process NAD is reduced to form NADH

39
Q

what happens during pyruvate decarboxylation?

A

Carbon atom is removed from pyruvate, forming CO2.
This converts pyruvate into a two-carbon molecule called acetate.
H+ is also removed from pyruvate in the conversion into acetate,
which is picked up by NAD to form NADH

(note: this is the first carbon which is lost from glucose in the process of converting glucose to 6CO2, 6H2O and energy)

40
Q

how does the PDH complex get regulated?

A

The PDH complex is activated by dephosphorylation- requires action of phosphatase
The enzyme is inactivated by phosphorylation- ATP is dephosphorylated to ADP catalysed by Kinase enzyme.

41
Q

why does the PDH complex need to be regulated?

A
  • Regulation means that TCA (Krebs) cycle is entered only when necessary
  • no waste as this reaction is irreversible
  • PDH complex converts pyruvate to acetyl CoA with production of CO2 & NADH
42
Q

Apart from glucose, what other molecules can generate acetyl CoA?

A

amino acids
fatty acids

43
Q

what happens to acetyl CoA when there’s excess dietary carbohydrates (its at high lvl) ?

A

it can be converted back to fatty acids and stored as energy for future use

44
Q

what is the carbon flux?

A

when amino acids are converted into acetyl co A
Acetyl CoA can also be formed from fatty acids via beta oxidation pathway generally in mitochondria at inner membrane surface
When Acetyl CoA levels are very high it can be converted into fatty acids for storage.

45
Q

what 2 enzymes is regulation based on in glycolysis and gluconeogenesis?

A

glycolysis- phosphofructokinase
gluconeogenesis- 1,6 bisphosphatase

46
Q

what is the citric acid cycle?

A

Occurs in mitochondrial matrix
The TCA cycle produces energy from all three major food groups (carbohydrates, proteins and lipids). They are all broken down and converted into Acetyl CoA which then enters this cycle.
Each cycle adds 2 C atoms as acetyl CoA which are then released in the form of 2CO2

47
Q

where is the energy of acetyl CoA stored?

A

NADH and FADH2

48
Q

where do the carbons lost in the cycle originate from

A

oxaloacetate
NOT acetyl coA

49
Q

what are the products from one cycle of TCA?

A

Acetyl COA –> CoA + 2CO2
3NAD+ –> 3NADH
FAD –> FADH2
GDP + Pi –> GTP (substrate lvl phosphorylation)

50
Q

what is oxygens role in metabolism?

A

final electron acceptor-
for NADH to lose electrons & NAD to return to the cycle
In the absence of O2 NAD+ & FAD cannot be regenerated so the anaerobic respiration pathway is followed

51
Q

what is NAD+ and where is it derived from?

A

It acts as a coenzyme in several redox reactions
Derived from the vitamin niacin (B3)

52
Q

how many ATPs does NAD+ generate?

A

It’s oxidation in the respiratory chain (electron transport chain i.e. loses H) generates 2.5 molecules of ATP

53
Q

what is FAD and where is it derived from?

A

It also acts as a coenzyme in several redox reactions
Derived from the vitamin riboflavin (B2)
FAD’s oxidation in succinate dehydrogenase generates 1.5 molecules of ATP (lower energy content of the electrons compare to NADH)

54
Q

what is FAD bound to?

A

FAD is covalently bound to Succinate dehydrogenase - as a prosthetic group
which itself is bound to the inner membrane of the mitochondria and is an integral part of the respiratory chain (electron transport chain).

55
Q

how many ATPs does FAD generate?

A

FAD’s oxidation in succinate dehydrogenase generates 1.5 molecules of ATP
(lower energy content of the electrons compare to NADH)

56
Q

what are anaplerotic reactions?

A

Anaplerotic reactions are reactions which fill in missing metabolites for important metabolic pathways

57
Q

what are anaplerotic reactions role in the TCA cycle?

A

they fill in the missing intermediates required for the TCA cycle
(dumbed down ver: they basically make different components of the TCA cycle without going through the cycle itself)

58
Q

what are examples of anaplerotic reactions in the TCA cycle?

A
  • Direct conversion of pyruvate to oxalacetate (PC reaction)
  • Aspartate <–> Oxaloacetate conversion (reversible depending on needs)
  • Glutamate <–> a-ketoglutarate conversion (reversible depending on needs)
  • Malate to pyruvate conversion (malic enzyme)
59
Q

what is the ETC composed of?

A

4 membrane complexes
2 mobile electron-carriers
coenzyme Q – hydrophobic 🡪 within lipid bilayer
cytochrome C – soluble 🡪 within cytosol of inner membrane space

60
Q

after glycolysis and TCA, how many FADH and NADH2 do we have?

A

for 1 glucose..
10 NADH- 6 from TCA, 2 from acetyl CoA formation, 2 from glycolysis
2 FADH2- from TCA

61
Q

what happens in the ETC (oxidative phosphorylation)?

A

1) NADH molecules gets oxidised and lose a proton and two electrons each
NADH + H+ –> NAD+ + 2H+ + 2e-
2) When the electrons leave NADH they are high in energy
3) Electrons then move through the complexes 1 and 3 embedded in the inner membrane- LOSING energy each time they’re passed on
4) This energy is used to pump protons (H+) across the inner mitochondrial membrane into the inter membrane space
5) The transport of 2 electrons through complex I and III will extrude 4 H+ each into the inter membrane space
6) During the proton pumping there are no counter ions pumped over the membrane
7) So in addition to a possible concentration gradient there is also a potential difference of around 150-250mV being produced. SO an electrochemical gradient is formed.
8) This potential difference provides the energy for ATP synthesis (chemiosmosis)
9) The H+ diffuse down their concentration gradient through ATP synthase back into the mitochondrial matrix. This result is the production of ATP by oxidative phosphorylation (ADP + Pi –> ATP)
10) Oxygen is the final electron acceptor - at the end of the electron transport chain the electrons combine with hydrogen ions and oxygen to from water.

62
Q

how many H+ ions are needed to make ATP?

A

3H+ ions are need to make 1 ATP
plus 1 H+ is needed translocate the ATP to the cytosol so 4 in total

63
Q

what catalyses the reaction between O2, H+ & e- and what can it be inhibited by?

A

Cytochrome C oxidase (complex 4) catalyses the transfer of the electrons to molecular oxygen
2e- + 2H+ + ½ O2 –> 2H2O
can be inhibited by cyanide, carbon monoxide and azide

64
Q

what is substrate level phosphorylation?

A

transfer of phosphate from a substate to ADP to form ATP (or GDP –> GTP)
without ETC

65
Q

what is oxidative phosphorylation?

A

formation of ATP coupled to oxidation of NADH or FADH2 by O2
with ETC

66
Q

what is the malate/ aspartate shuttle and the glycerol phosphate shuttle used for?

A

NADH molecules formed during glycolysis are located in the cytosol
However, NADH can only be oxidised INSIDE the mitochondria and NADH are unable to cross the mitochondrial membrane
there are no transporters that would transport NADH from cytosol to the mitochondria

67
Q

what are the 2 mechanisms used to convert NADH back to NAD+?

A

the malate/ aspartate shuttle (used in humans)
the glycerol phosphate shuttle (mainly used in insects)

68
Q

what happens in the glycerol phosphate shuttle?

A

Uses cytosolic NADH to reduce DHAP to form glycerol-3-phosphate (now has an extra H)
which then diffuses into the mitochondria and is oxidised by mitochondrial glycerol-3-phosphate dehydrogenase to form DHAP and FADH2

69
Q

what happens in the malate/ aspartate shuttle?

A

1) malate dehydrogenase reduces oxaloacetate to form malate (has gained a H+), which is then transported into the inter membrane space of the mitochondria.
2) Inside the intermembrane space, the reaction is simply reversed by the mitochondrial malate dehydrogenase – malate –> OAA and the H+ is given to NAD+ forming NADH.
3) However as OAA is unable to cross the inner mitochondrial membrane it has to be transaminated to aspartate which can then be transported into the cytosol, where it is converted back into OAA by the cytosolic aspartate aminotransferase
4) While usually 10 H+ per NADH can be pumped across the membrane to form ATP, in this case the glutamate aspartate carrier (to maintain glutamate and aspartate concentrations) uses 1 H+.
Hence the ATP production is only 2.25 molecules of ATP per cytosolic NADH (9/4 = 2.25)

70
Q

how many ATP molecules do you get from one molecule of glucose?

A

it depends on what you use- could be 31, 38 or 36
P/O ratios: the number of ATP molecules synthesised per O2 consumed
Historically these were integers (3 for NADH, 2 for FADH2)
However, oxidation of NADH leads to extrusion of a total of 10 H + ions - 2.5 molecules ATP
Similar for FADH2, except it is only a total of 6 H+ - hence 1.5 ATP
In eukaryotes, remember cytosolic NADH loses another due to the malate / aspartate shuttle
Using the historic P /O ratios gives a total of 38 molecules of ATP generated
Using the modern non-integer P / O ratios yield a total of 31 ATP for eukaryotes using the malate/ aspartate shuttle and 29.5 ATP using the glycerol phosphate shuttle
unaware of which number is correct- could be that systems are very tightly coupled in vivo leading to a much higher efficiency of the proton pumping

71
Q

what is special about mitochondria in brown adipose tissue?

A
  • Rare in comparison compare with white fat
  • Mitochondria in brown adipose tissue are largely uncoupled (movement of protons through proton channels back into matrix is not coupled to ATP synthesis so no ATP is produced)
    so energy (stored in proton and electrochemical gradient) released as heat rather than captured as ATP
    Brown adipose is therefore important for maintaining body temperature, especially in neonates
    Uncoupling proteins (UCP) provide proton channel
    Dinitrophenol is also a uncoupler 🡪 dissipates the proton gradient
72
Q

what is brown adipose tissue important for?

A

Important for maintaining body temperature, especially in neonates (newborns)
Uncoupling proteins (UCP) provide proton channel
Dinitrophenol (drug) is also a uncoupler- dissipates the proton gradient

73
Q

In addition to glucose, what else can be used to produce ATP?

A

fatty acids- although its a slow process
proteins- to release AA which are broken down further to produce ATP by reversing pathways in the TCA cycle
lactate- some cells in the brain only break down glucose into lactate which is then secreted and neighbouring cells take up the lactate, converting it into pyruvate- it then enters TCA cycle

74
Q

what are the 3 controls of metabolism?

A

primary control - the level of ATP
level of intermediates affect local rates

enzyme level
enzyme activities
substrate availability

75
Q

what does an enzyme level mechanism control?

A

An enzyme level mechanism controls uptake of glucose via GLUTS
Levels of GLUTs not static - dependent on tissue activity (i.e. levels of GLUT4 increases in muscles with endurance training)
Different tissues have different GLUTS
Different Gluts have different affinities for glucose, the lower the KM the higher the affinity for glucose so they can take up glucose more easily.

76
Q

what is an example of enzyme activity control?

A

phosphofructokinase inhibited by high ATP levels and citrate (indicating enough energy) and activated by AMP (signalling lack of energy).
Once activated it converts Fructose 6 – phosphate to Fructose 1,6-bisphosphate
glycolysis starts & gluconeogenesis pathway stopped.

77
Q

how is substrate availability controlled?

A

Pyruvate dehydrogenase, isocitrate dehydrogenase, & α-ketoglutarate dehydrogenase are the control points of the TCA cycle
They are all inhibited by ATP, NADH, and acetyl CoA (substrates - all indicate enough energy or there is a blockage in cycle or acetyl CoA can’t be used up fast enough)

78
Q

how much energy does the brain consume at rest?

A

consumes —60% of body glucose at rest.
Can use ketone bodies in starvation and sometimes use lactate

79
Q

how much energy does the muscles consume at rest?

A

Resting muscle uses fatty acids.
During exercise muscle respires anaerobically 🡪 uses glycogen stores to produce lactate

80
Q

how much energy does the kidney consume?

A

0.5% of body mass but use 10% of body glucose (Na+ K+ ATPase)

81
Q

what are the diseases associated with defects in carbohydrate metabolism?

A

Range of diseases resulting from mitochondrial defects (neuro/visual symptoms) i.e.
- Leber hereditary optic neuropathy (complex I – electron transport chain)
- Beriberi - VitB1 deficiency. B1 is a cofactor for Pyruvate Dehydrogenase and α-ketoglut Dehydrogenase)
- Mercury & Arsenic poisoning decrease Pyruvate Dehydrogenase activity and GAP –> 3PGA conversion
- Diabetes mellitus – inability to take in glucose due to lack of insulin or insulin insensitivity
- Glycogen storage disease (e.g. von Gierke’s (lack of glucose 6-phosphatase), McArdle’s myophosphorylase deficiency, Tarui - PFK; cori; others deficiency
- Cancer (metabolomics; PKM2) 🡪 cause system wide deregulation of metabolism

82
Q

how do ATP levels control insulin secretion?

A

Beta cells have special glucose transporter which takes in glucose
Glucose converted into ATP
ATP induces insulin release into blood stream
ATP levels controls insulin secretion (high ATP = more insulin released)
In Type 1 diabetes enough insulin is not prodcued which results in ketone body production - ketoacidosis.
high blood glucose and excessive ketone body production

leading to acidosis, coma, death

83
Q

what is the Warburg Effect in cancer?

A

Tumour cells favour lactate fermentation even in presence of O2
This method is not only less efficient in ATP production than aerobic respiration but also produces many metabolites which favours rapid proliferation of cells therefore rapid growth of tumour

Semester 1- MTM (15 decks)

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