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Y1 Genes, Molecules and Cells > Metabolism > Flashcards

Metabolism Flashcards

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1
Q

What is the key purpose of glycolysis

A
  • Employed by all tissues for glucose oxidation to provide energy (ATP)
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2
Q

With an adequate supply of oxygen (+mitocondria)…

A
  • Pyruvate is the end product
  • Aerobic glycolysis as O₂ required to reoxidise NADH
  • Oxidative decarboxylication of pyruvate to acetyl-CoA (which is then used in the TCA cycle)
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3
Q

Without an adequate supply of oxygen (+mitocondria)…

A
  • Anaerobic glycolysis
  • Pyruvate is reduced to lactate as NADH reoxidised
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4
Q

How can glucose enter cells as it is two large to diffuse

A

There are two methods:
* Na⁺ - independent facilitated diffusion transport
* ATP-dependent Na⁺-monosaccharide transport

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5
Q

Describe the process of Na⁺-independent facilitated diffusion

A
  • Glucose moves via concentration gradient
  • Glucose bind to the GLUT transporter and is moved through the membrane
  • These transporters exhibit tissue-specific expression (GLUT 1-14)
  • This type of transport relies on there being a concentration gradient (e.g. not possible for cells with a large amount of glucose within them)
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6
Q

Describe the process of ATP-dependent Na⁺-monosaccaride transport system

A
  • A co-transport system
  • Transports glucose against a concentration gradient (coupled to Na⁺ gradient)
  • Found in intestinal epithelial cells
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7
Q

Conversion of glucose to pyruvate occurs in two stages, what are they?

A
  1. The energy investment phase (first 5 reactions): phosphorylated forms created using ATP
  2. Energy generation phase
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8
Q

What is the first step of glycolysis and why does it occur

A

Phosphorylation of glucose
Phosphorylated sugar molecules don’t cross cell membranes easily
irreversible phosphorylation of glucose traps it in cytosol and commits it

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9
Q

What is the enzyme that catalyses the reaction of glucose phosphorylation?
What type of enzyme is it?
What it its Km and Vmax like?

A

Hexokinase (l-lll)
Allosterically regulated enzyme of glycolysis (can be inhibited by glucose-6-phosphate)
Low Km (high affinity for glucose)
Low Vmax (means no overabundance of glucose-6-phosphate)

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10
Q

What is Glucokinase and how does it relate to the consumption of different foods

A
  • Glucokinase is a form of Hexokinase (iv)
  • It has a high Km (low affinity) so only active following consumption of carb-rich meals
  • High Vmax allowing glucose delivered to liver to be maximally absorbed
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11
Q

What is the second step of glycolysis

A
  • Isomerisation of glucose-6-phosphate to fructose-6-phosphate
  • Catalysed by phosphoglucose isomerise
  • Readily reversible + not rate limiting
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12
Q

What is the 3rd step of glycolysis

A
  • Another phosporylation
  • Fructose-6-phosphate is phosphorylsed to form Fructose-1,6-bisphosphate
  • Irreversible reaction
  • Catalysed by phosphofructokinase-1
  • Most important control point
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13
Q

In step no3 of glycolysis, where Fructose-6-phosphate is phosphorylate, why is this considered an important control step

A

Because the enzyme phosphofructokinase-1 (PFK-1) is controlled by ATP and allosterically through fructose-6-phosphate
* High amount of ATP will cause inhibition of step 3, as it indicates high amount of energy available
* High amount of AMP will cause activition as ATP has be dephosphorylated - energy deficition
Also inhibited by citrate from the TCA, as high amount of this indicate a lot of energy

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14
Q

What happens in steps 4 and 5 of glycolysis

A
  • Aldolase cleaves fructose-1,6-bisphosphate to form Dihydroxyacetone phosphate (DHAP) and Glyceraldehyde-3-phosphate
  • Reversible and unregulated
  • Triose phosphate isomerise allows interconversion of DHAP to form Glyceraldehyde-3-phosphate
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15
Q

What other cellular process is Dihydroxyacetone phosphate (DHAP) involved in

A

Triacylgycerol synthesis
As only glyceraldehyde-3-phosphate (GAP) can be used in glycolysis)

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16
Q

What happens in step 6 in glycolysis

A
  • Oxidation-reaction reaction: adds a phosphate group and removes two electrons forming NADH
  • Two molecules of glyceraldehyde-3-phosphate are converted into 1,3-bisphosphoglycerate (1,3-BPG) using glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
  • Drives the synthesis of ATP in the next reaction
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17
Q

What happens in step 7 of glycolysis

A
  • Substrate-level phosphorylation
  • Forms** two 3-phosphoglycerate** from two 1,3-bisphosphoglycerate and two molecules of ATP
  • The ATP produced replaces the ATP consumed earlier
  • Catalysed by physiologically reversible enzyme
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18
Q

What happens in step 8 of gylcolysis

A
  • Forms 2-phosphoglycerate
  • Phosphoglycerate mutase shifts the phosphate from carbon 3 to 2
  • Reversible reaction
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19
Q

What happens in step 9 of glycolysis

A
  • Forms Phosphoenolpyruvate
  • Enolase redistributes the energy within the molecule by dehydration
  • Reversible reaction
  • Creates a high energy intermediate
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20
Q

What happens in step 10 of gylcolysis

A
  • Forms pryuvate
  • Catalysed by pryuvate kinase
  • Irreversible reaction of glycolysis
  • Substrate level phosphorylation forming two molecule of ATP
  • Links with the Fructose-1,6-bisphosphate to regulate the speed of this reaction
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21
Q

What is TARU disease

A

Where phosphofructokinase-1 isn’t functioning optimally, so sufferers tend to utilise the build up of metabolites before phosphofructokinase-1 and they end-up creating a large amount of glycogen
Glycogen storage disease

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22
Q

How is Haemolytic anemia related to glycolytic enzyme deficiencies

A
  • Deficiencies in pryuvate kinase, which impact RBC mortality
  • RBC are biconcave, where the shape is dependent on the ability to maintain the activity of iron pumps
  • Without this the RBC change shape, there is failure to generate ATP and phagocytosis of RBC will occur
  • Suffers require regular transfusions
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23
Q

Pyruvate is the product of glycolysis
Without the presence of oxygen (+mitocondria) anerobic respiration occurs, how?
(This most likely occurs in RBC, testes and respiring muscle, cornea)

A
  • Pyruvate is reduced to lactate by lacatate dehydrogenase
  • Lactate dehydrogenase reaction direction depends on metabolite concentration + NADH/NAD⁺ ratio (low ratio casues latate to be oxidise e.g. in liver)
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24
Q

What are the 3 likely outcome for pyruvate

A
  1. Oxidiative decarboxylation into Acetyl CoA (Pyruvate dehydrogenase): major fuel for TCA cycle + fatty acid synthesis
  2. Carboxylated to oxaloacetate (Pyruvate carboxylase): Replenishes TCA cycle intermediates + substrate fpr gluconeogenesis
  3. Reduced to ethanol (yeast)
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25
Q

How can the regulation of those 3 outcomes be controlled in the short-term

A

Short-term regulation (mins/hrs) by allosteric activation/deactivation
phosphorylation/dephosphorylation of kinases

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26
Q

How can the regulation of those 3 outcomes of pryuvate be controlled in the long-term

A

Hormones can determine the amount of enzyme produced effecting the amount of pryuvate formed
e.g. if there is a sudden increase in carbs in a diet, increase transcription of glucose kinase/pryuvate kinase etc

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27
Q

The TCA cycle is the next stage
What does TCA stand for

A

Tricarboxlic Acid Cycle
Also know as ‘Critic Acid Cyle’ or ‘Krebs Cycle’

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28
Q

The TCA cycle is the next stage
What does TCA stand for

A

Tricarboxlic Acid Cycle
Also know as ‘Critic Acid Cyle’ or ‘Krebs Cycle’

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29
Q

What are the roles of the TCA cycle

A
  • Where oxidative catabolism of carbohydrates, amino acids, and fatty acids converge
  • Produces most of the ATP found in Humans
  • Supplies intermediates for synthetic reactions (e.g. heme)
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30
Q

Where does the TCA cycle occur?
What is the main function of it for the production of energy?
What does it require?

A

Occurs in the Mitocondria (close to the ETC)
Allows oxidation of NADH and FADH₂
Requires Oxygen

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31
Q

Glycolysis occurs within the cytosol, then the product pyruvate must be transported into the mitocondria by a transporter
What happens next?

A

Pryuvate is then coverted to acetyl CoA by the pyruvate dehydrogenase complex

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32
Q

PDH complex is aggregate of 3 enzyme types
What are they

A
  1. Pyruvate carboxylase
  2. Dihydrolipoyl transacetylase
  3. Dihydrolipoyl dehydrogenase
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33
Q

What is Leigh syndrome

A

Mutations in the Pyruvate dehydrogenase complex (PDH)
Progressive neurological disorder
Defects in mitocondrial ATP production

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34
Q

What happens within the first step of the TCA cycle

A
  • In the first reaction oxaloacetate is first condensed with an acetyl group from acetyl coenzyme A
  • This forms Critrate
  • Catalysed by Citrate synthase
  • Reaction is regulated by product and substrate (allosteric regulation)
  • Equilibrium favour the forwards reaction
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35
Q

What happens in the second step of the TAC cycle

A
  • Citrate is isomerised to form Isocitrate
  • Catalysed by Aconitase
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36
Q

What happens in the 3rd step of the TAC cycle

A
  • Isocitrate is oxidised + decarboxylated to form α-Ketoglutarate
  • Catalysed by Isocitrate dehydrogenase (encoraged by ADP)
  • Irreversible = rate limiting
  • Yeilds NADH
  • Releases CO₂
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37
Q

What happens in step 4 of the TAC cycle

A
  • α-ketoglutarate is oxidatively decarboxylared forming Succinyl-CoA
  • Catalysed by α-ketoglutarate dehydrogenase complex
  • Produces NADH + CO₂
  • Equilibrium favours the forward reaction
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38
Q

What happens in step 5 of TAC cycle

A
  • Succinyl Co-A is cleaved at the high-energy thioester bond forming Succinate
  • Catalysed by Succinate Thiokinase
  • Substrate level phosphorylation of GDP, which is then interconverted to ATP by nucleoside diphosphate kinase
39
Q

What happens in Step 6 of the TCA cycle

A
  • Succinate is oxidised to fumarate
  • Catalysed by Succinate dehydrogenase
  • FAD is reduced to FADH₂
40
Q

What happens in Step 7 of the TCA cycle

A
  • Fumarate is hydrated to Malate
  • Catalysed by Fumerase
  • Reversible reaction
41
Q

What happens in Step 8 of the TCA cycle

A
  • Malate is oxidised to oxaloacetate
  • Catalysed by malate dehydrogenase
  • Produces final NADH
  • Needs an input of energy (endgergonic)
42
Q

What is the overall output of the TCA cycle

A

2 carbon atom enter as Acetyl Co-A (and leave as CO₂)
3 NADH and 1 FADH₂ are formed

43
Q

How is the TCA cycle controlled

A

It is controlled by serveral enzyme:
* Citrate synthase
* Isocitrate dehydrogenase
* α-ketoglutarate dehydrogenase complex

44
Q

How many ATP are producer per molecule of NADH and molecule of FADH₂

A
  • 3 ATP per NADH
  • 2 ATP per FADH₂
45
Q

What is Metabolism

A
  • Is the process by which living systems acquire + use free energy in order to carry out their functions
46
Q

What are the two tradition divisions of metabolism

A

Catabolic and Anabolic

47
Q

What is the difference between catabolic and anabolic metabolism

A
  • Catabolic: The degradation of nutrients to salvage componets + gain energy (using carbs, fats + proteins)
  • Anabolic: The synthesis of biomolecules from simpler componets (forming biological molecules)
48
Q

Metabolism involves many highly complicated reaction, what, however, are the two main principles that govern them all?

A
  • Common evolutionary origin
  • Laws of Thermodynamics
49
Q

What are Autotrophs?
What are the two types of autotrophs?

A

Autrotrophs: Synthesise all cellular componets from simple molecules
Two types: Photoautotrophs and Chemolithotrophs

50
Q

What is a Photoautotroph

A

Photoautotrophs: use light energy to produce carbohydrates which are oxidised giving free energy

51
Q

What is a Chemolithotrophs

A

Obtain free energy from inorganic compound oxidation (NH₃, H₂S)

52
Q

What are Heterotrophs

A

Oxidise carbohydrates, lipids and proteins (gained from other ‘trophs’)

53
Q

Obligate aerobes use what for oxidation?

A

Oxygen

54
Q

Anerobes use what as oxidising agents

A

Sulfate or nitrate

55
Q

What two things bar oxygen are needed by obligate aerobic heterotrophs

A
  • Macronutrients (lipids, carbs and proteins)
  • Micronutrients to help with metabolism of breakdown products: including vitamins (organic molecules obtained from diet) and minerals (ions)
56
Q

As well as polysaccharides, what else can enter into glycolysis or TAC cycle at different points

A

Proteins and Triglycerols
They are known as degradative pathways

57
Q

What is a biosynthetic pathways

A

They carry out the opposite of a degradative pathway

58
Q

What are the benefits of enyzmes in metabolism reactions

A
  • Without enzymes metabolic reactions would occur far to slowly
  • Specificity prevents useless or toxic product formation
  • Couples endergonic reaction with energetically favourable reactions
59
Q

What are the 4 types of reactions seen in metabolism reactions?

A
  • Oxidation + Reduction
  • Group transfer reactions
  • Eliminations, isomerisations + rearrangements
  • Carbon-Carbon bond breakage
60
Q

Some reactions have a -ΔG
What does this mean

A

The reaction is spontaneous and favourable

61
Q

Some reactions have a ΔG = 0
Meaning?

A

This reaction is at equilibrium

61
Q

Some reactions have a ΔG = 0
Meaning?

A

This reaction is at equilibrium

62
Q

Some metabolic reactions are highly spontaneous (-ΔG) some are not
What is the benefit of this

A

Enzymes can coupled these reactions together and the energy for one can provide the energy for another

63
Q

Oxidative metbolism proceeds in a step-wise fashion
What is the benefit of this?

A
  • Released energy can be recovered at each exergonic step
  • This energy is conserved as ‘high-energy’ intermediates
64
Q

Give some examples of cellular energy currency

A
  • Thioester bond-containing compounds
  • Reduced coenzymes
  • ATP
65
Q

What is a co-enzyme

A

As metabolic fuels are oxidised to CO₂, electrons are transferred to molecular carriers. Often in oxidation-reduction reactions

66
Q

Which are the most common two co-enzyme (electron carriers)

A
  1. Nicotinamide Adenine Dinucleotide (NAD⁺)
  2. Flavin Adenine Dinucleotide (FAD)
67
Q

Explain the reaction to convert NAD⁺ in its oxidised form into NADH in its reduced form

A

NAD⁺ + 2H⁺ + 2e⁻ → NADH + H⁺

68
Q

Explain the reaction to convert FAD in its oxidised form into FADH₂ in its reduced form

A

FAD + + 2H⁺ + 2e⁻ → FADH₂

69
Q

The energy in ATP comes from

A

ATP’s biological importance depends on the free energy change that accompanies cleavage of the phosphoanhydride

70
Q

Where is the electron transport chain located

A

Inner mitocondrial membrane

71
Q

In an overview, however is ATP synthesised in the electron transport chain

A
  • Reduced co-enzyme can donate electrons pairs to electron carriers in the Electron transport chain located in the inner mitocondrial membrane
  • As the electrons pass down the ETC, they loose free energy
  • Used to move protons across the inner mitocondrial membrane
  • Creates a proton gradient which drives ATP synthesis from ADP and Pi
72
Q

The inner mitochondrial membrane contains how many protein complexes

A

5 separate protein complexes
Complexes l, ll, lll , lV, V

73
Q

There are two mobile electron carrier
What are they called?

A
  • Coenzyme Q
  • Cytochrome C
74
Q

What is the use of oxygen in the electron transport chain

A

Oxygen is the terminal electron acceptor, where they combine to form water
This accounts for the greatest porption of the body’s oxygen use

75
Q

What happens at complex l

A
  • NADH binds to the complex and electrons are transferred to CoQ
  • Electrons energy is lost, as it is used to pump 4 protons across the inner membrane
76
Q

What are the two used of complex ll

A
  • Accepts electrons from FADH₂ and transfers them to CoQ via Fe-S proteins
  • No energy is lost, hence no protons are pumped at complex ll
  • Contains succinate dehydrogenase which catalyses succinate to fumarate in TCA cycle
77
Q

What is the hindrance around cytochrome c

A

It only can recieve one electron at a time
Hence CoQ and complex lll transfer electrons between another to meet this requirement

78
Q

What is Coenzyme Q

A

It is a small lipid soluble compound - hydrophobic quinone
Which diffuses rapidly with IMM

79
Q

What is Coenzyme Q

A

It is a small lipid soluble compound - hydrophobic quinone
Which diffuses rapidly with IMM

80
Q

Both Complex III and Cytochrome C are known as…
Why?

A

Cytochrome proteins
contain a heme group

81
Q

Cytochrome C is a peripheral protein meaning?

A

membrane proteins that adhere only temporarily to the biological membrane with which they are associated

82
Q

How does electron movement occur between Complex lll and Cyt C

A

Complex 3 transfers electrons to Cyt C which then transfers them to Complex lV
At Complex lll energy is lost which is used to pump 4 protons across the inner membrane

83
Q

What happens at Complex lV

A
  • This electron carrier has a co-ordination site for O₂ within the heme group
  • Transfers a pair of electrons to 0.5O₂ which is reduced to form H₂O
  • 2 electrons are pumped across inner mitocondrial membrane
84
Q

The transfer of electrons down the ETC has a ΔG = -52.6 kcal mol⁻¹
Meaning?

A
  • The transfer of electrons down the ETC is energetically favourable
  • NADH is a strong electron donor (reducing agents)
  • O₂ is a strong electron acceptor (oxidising agent)
85
Q

What is the Chemiosmotic hypothesis

A

Proton pumping across the inner mitocondrial membrane creates a proton gradient (more +ve change on the outside than inside)
This drives ATP synthesis via ATP synthase (complex V)

86
Q

How does ATP synthase (Complex V) operate

A
  • Protons pumped to the cytosolic side of mitocondrial membrane re-enter the matrix by passing through F0 proton channel
  • As protons pass down the channel they drive the rotation of the C ring of F0 which causes a conformational change in the β-subunit of the F1
  • ADP and Pi bond and ATP is formed and released
87
Q

For every pair of electrons from NADH and FADH₂, how many ATP are generated

A

NADH: 2.5 ATP
FADH₂: 1.5 ATP

88
Q

From 1 glucose molecule, how many ATP can be generate

A

30 ATP generated by oxidative phosphorylation
(Compared to 2 from glycolysis)

89
Q

Inhibitors of the electron transport chain, do what?

A

Prevent the passage of electrons down the ETC and so prevent protons being pumped across the inner mitocondrial membrane
Hence inhibiting ATP synthesis

90
Q

What complex does cyanide, azide and CO effect

A

Complex lV

91
Q

How do uncoupling proteins affect ATP synthesis

A
  • Created a pore across the membrane and hence a dissipation of the proton gradient BUT the ETC will still be operational
  • The free energy will be dissipated as heat
92
Q

Why do some organisms not due O₂ as the terminal electron acceptor

A

Allow these organisms to live in anaerobic environments e.g. soil, hydrothermal vents, bottom of lakes

Y1 Genes, Molecules and Cells (16 decks)

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