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104: Theme 2 > Cellular Biochemistry > Flashcards

Cellular Biochemistry Flashcards

2-5

1
Q

Define Anabolism

A

Synthetics reactions the pathways end in ‘genesis’

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2
Q

Define Catabolism

A

Breakdown reactions, pathways end in ‘lysis’

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3
Q

What is the purpose of ‘free energy’?

A
  • provides cells energy to function where heat flow cannot
  • this is because cells have to remain in an isothermal state
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4
Q

Gibbs Free Energy

A

G= ∆H- T∆S

when G= 0 : reaction is just feasible

when G < 0 : reaction is feasible, catabolism, exo

when G > 0 : reaction isn’t feasible, Anabolism, endo

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5
Q

Explain coupling reactions and their use,

A
  • coupling an endergonic reaction with an exergonic reaction to make it spontaneously feasible where total ∆G < 0
  • this is done through a common intermediate
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6
Q

Give an example of a coupling reaction?

A

Glucose + Pi → glucose-6-phosphate + H2O

ATP + H2O → ADP + Pi

Glucose+ ATP → ADP + glucose-6-phosphate

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7
Q

Describe and explain Phosphate Group Transfer

A
  • the manner in which ATP provides most of the free energy that is required of it
  • during reactions, phosphate group forms a covalent bond with a species on the molecule
  • this bond is then displaced by another more reactive species forming the new molecule and as lose in a Pi molecule
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8
Q

What is the role of Mg2+ with ATP/ADP?

A
  • forms a complex with ATP in the cytosol
  • interacts with oxygen on triphosphate chain making it susceptible to nucleophilic attack, ( species that are rich in é will attack it)
  • Mg2+ deficiency impairs metablosim
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9
Q

What is substrate-level phosphorylation and how is it different from respiration-linked phosphorylation?

A
  • formation of ATP by phosphate group transfer from a substrate to ADP
  • requires a soluble enzyme and a chemical intermediate

whereas

RLP involves membrane-bound enzymes and transmembrane gradients of protons and requires oxygen (Krebs Cycle)

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10
Q

What are the 6 main classes of enzymes?

A
  1. Oxidoreductases ( transfer Oil Rig)
  2. Transferases (of functional groups)
  3. Hydrolases ( just add)
  4. Lyases (syntheses) ( cleavage or formation of bonds)
  5. Isomerases (transfer of groups within a molecule)
  6. Ligases (synthetases) (Bond formation coupled to ATP hydrolysis)
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11
Q

What are co-factors?

A
  • non-protein parts that are essential for the function of an enzyme

split into

  • metal ions
  • coenzymes
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12
Q

What are coenzymes?

A
  • participate in the enzymatic reaction
  • diffuse between enzymes carrying enzymes é
  • cycle between oxidised and reduced forms
  • usually derived from vitamins
  • divided into cosubstrates and prosthetic groups
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13
Q

What is the difference between a prosthetic group and a co-substrate?

A

Co-substrate: loosely associated with the enzyme

Prosthetic group: always covalently bound to the enzyme, not released as part of the reaction

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14
Q

What is a vitamin precursor for a prosthetic group?

A

Vitamin B2 (Riboflavin) → FAD or FMN

Flavin Adenine Dinucleotide

Flavin Mononucleotide

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15
Q

What is a vitamin precursor for a cosubstrate?

A

Niacin → NAD+

Nicotinamide Adenine Dinucleotide

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16
Q

What is the role of coenzymes in Redox?

A
  • act as oxidizing agents during respiration
  • NAD+ → NADH : gains 2é and one H+ ion
  • FAD → FADH : gains 2é and 2H+ ions
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17
Q

What is the role of NADH and NADPH?

A
  • NADH → ATP synthesis
  • NADPH → reductive biosynthesis (anabolic biosynthetic reactions)
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18
Q

What are the enzymes involved in the priming stages of glycolysis? Fill in the blanks of the diagram.

A

Hk: Hexokinase

Isomerase

PFK-1: phospho-fructose kinase

ALdolase

Isomerasew

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19
Q

What are the enzymes involved in the glycolysis payoff reactions? Fill in the gaps

A

GAPDH: G3P dehydrogenase

PGK: Phosphoglycerate kinase

Mutase: PG mutase

Enolase

PK: Pyruvate kinase

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20
Q

How pyruvate transported into the mitochondrion?

A
  • travels through a carrier protein embedded in the MM
  • Irreversible Link Reaction* between glycolysis and the TCA
  • oxidative decarboxylation by the pyruvate dehydrogenase complex → Acetyl CoA

Pyruvate + CoA + NAD+ → Acetyl CoA + CO2 +NADH + H+

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21
Q

What constitutes the pyruvate dehydrogenase complex? And which vitamins are vital to four of these complexes?

A

3 enzymes

5 coenzymes

  • Thiamine pyrophosphate (TPP): Thiamine
  • NAD+: Niacin
  • CoA: Pantothenate
  • FAD: Riboflavin
  • Lipoic acid
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22
Q

A Class In Kama Sutra Should Further My Orgasm

What are the 8 intermediates in the TCA cycle? Fill in the blanks

A

Acetyl CoA: 2C

Citric Acid: 6C

Isocitrate: 6C

alpha Ketoglutarate: 5C

Succinyl CoA: 4C

Succinate: 4C

Fumarate: 4C

Malate: 4C

Oxaloacetate: 4C

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23
Q

How is the floc of Carbon atoms regulated in the TCA cycle?

A
  • conversion of pyruvate to acetly-CoA (PDH reaction)
  • entry of acetyl-CoA into the TCA cycle ( citrate synthase reaction)

Also regulated at isocitrate dehydrogenase and apha ketoglutarate dehydrogenase reactions

  • these reactions are irreversible
24
Q

Give two important biosynthetic intermediates of the TCA cycle and explain how they are replenished

A
  • Oxaloacetate: 4C that combines with Acetyl-CoA to form Citrate also converts to PEP to make amino acids
  • Malate the precursor to Oxaloacetate

Oxaloacetate is replenished by

  • Pyruvate using pyruvate carboxylase
  • Phosphoenolpyruvate (PEP) using PEP carboxykinase and PEP carboxylase

Malate is replenished by

Pyruvate using malic enzyme

25
Q

How do the electrons in NADH enter the inner mitochondrial membrane?

A

Via electron shuttles

  • Glycerol-3-phosphate shuttle largely prevalent in the brain and muscle
  • the Malate-aspartate shuttle in the liver and heart
  • regenerate NAD+
26
Q

Explain the glycerol-3-phosphate shuttle.

Fill in the diagram

A
27
Q

Explain the Malate-aspartate shuttle.

Fill in the diagram

A
28
Q

What happens in the link reaction in the Krebs Cycle?

A
  • Pyruvate loses a CO2 molecule: oxidative decarboxylation
    • the pyruvate dehydrogenase complex catalysts this reaction
  • this forms Acetyl CoA
    • releases CO2 and NADH + H+

This is an irreversible reaction, takes place in the matrix of the mitochondria after pyruvate has crossed the inner mito. membrane

29
Q

What makes up the pyruvate dehydrogenase complex?

A
  • Three difference enzymes
  • Five different coenzymes
    • Thiamine pyrophosphate: TPP
      • vitamin Thiamine
    • NAD+
      • vitamin Niacin
    • CoA
      • vitamin Pantothenate
    • Flavine Adenine Dinucleotide: FAD
      • vitamin Riboflavin
      • Lipoic acid
30
Q

How does pyruvate enter the mitochondrion from the cytosol?

A
  • enters via MPC: Mitochondrial Pyruvate carrier
  • this is embedded into the inner mitochondrial membrane
31
Q

What are the products of the TCA cycle?

A
  • 3x NADred
  • 1x FADred
  • 2x CO2
  • 1x GTP: guanosine-5-triphosphate, later converted to ATP
32
Q

A Class In Kama Sutra Should Further My Orgasm

What are the intermediates of the TCA cycle?

A
  • oxaloacetate is regenerated and binds to acetyl CoA to form citrate which is the “start” of the cycle
  • Acetyl CoA
  • Citrate
  • Isocitrate
  • alpha-Ketoglutarate
  • Succinly CoA
  • Succinate
  • Fumarate
  • L-Malate
  • Oxaloacetate
33
Q

What are the rate-controlling enzymatic steps in the TCA cycle?

A
  • oxaloacetate is regenerated and binds to acetyl CoA to form citrate which is the “start” of the cycle
  • the condensation reaction between Acetyl CoA and Oxaloactetate
    • this forms Citrate: reaction catalysed by citrate synthase
  • Oxidative decarboxylation of Isocitrate
    • this forms alpha-Ketoglutarate: reaction catalysed by isocitrate dehydrogenase
  • Oxidative decarboxylation of alpha-Ketoglutarate
    • this forms Succinyl CoA: reaction catalysed by alpha dehydrogenase
34
Q

What are the two main ways the TCA cycle is regulated?

A
  • conversion of pyruvate into acetyl-CoA: Pyruvate dehydrogenase reaction
  • the entry of acetyl-CoA into the TCA cycle: the citrate synthase reaction

^ acetyl-CoA could be used to build lipids instead

( isocitrate and alpha-Ketoglutarate reactions are also a way of controlling the rate of reaction)

35
Q

What are the two shuttles that transport the electrons of NADH into the mitochondrion?

A
  • The Glycerol-3-phosphate shuttle: largely prevalent in brain and muscle
    • G-3-P dehydrogenase oxidises NADred to NAD+ and reduces DHAP into G-3-P
    • G-3-P can enter mitochondria and the electron is used to reduce FAD to FADH2
  • The malate-aspartate shuttle: in the liver and heart
    • aspartate leaves the mitochondria converted to oxaloacetate by alpha-KG
    • oxaloacetate is reduced to malate which enters mitochondria exchanged with alpha-KG
    • malate oxidizes back to oxaloacetate
    • oxaloacetate to separate using glutamate from outside the mitochondria converted to alpha-KG again
    • aspartate leaves to restart the shuttle
36
Q

What are the components that make up the ETC?

A
  • Complex I to IV
    • Complex I: NADH dehydrogenase
    • Complex II: Succinate dehydrogenase
    • Complex III: Ubiquinonep cytochrome c oxidoreductase
    • Complex IV: Cytochrome oxidase
  • Complexes linked by 2 soluble proteins
    • Ubiquinone (coenzyme Q): can move within the IMM
    • Cytochrome c

Complex I, III, IV are proton pumps from the matric into the intramembrane space. these are used for further red. of NAD+ and FAD

37
Q

What is the action of Complex I?

A
  • Reaction: NADH +H+ + Q = NAD+ + QH2
    • the H+ is lost to FMN to form FMNH2
    • eventually is transferred to coenzyme Q- ubiquinone
  • overall acts as a proton pump from the matrix into the intramitochondrial space
38
Q

What is the action of Complex II?

A
  • aka Succinate dehydrogenase
  • electrons of FADH2 transfer their electrons to complex to
    • this is then passed on to ubiquinone (Q) to form QH2
    • Succinate –> Fumarate
39
Q

What are other sources of electrons for the ETC?

A
  • through Beta-oxidation of lipids
  • cytosolic Glycerol 3-phosphate
40
Q

What is the action of Complex III and IV?

A
  • Complex III: Ubiquinone: cytochrome c oxidoreductase
    • 2nd of 3 proton pumps in ETC
  • Complex IV: Cytochrome oxidase
    • final proton pump
    • terminal electron accepter
    • produced water
41
Q

What is the impact of the Complexes in the ETC?

A
  • Complex I and III transfer 4 protons into he intramembrane space
  • Complex IV transfers 2
    • the combined effect creates a very positive electrochemical gradient in the intramembrane space
  • this allows ADP3- from the matrix to be exchanged for ATP<strong><u>4-</u></strong> from the intramembrane space
    • this is carried out by the antiporter Adenine nucleotide translocase
42
Q

What is the Adenine nucleotide translocase?

What is it’s action?

A
  • antiporter
  • facilitates the exchange of ADP from the matrix and ATP from the intramitochondrial space
    • the antiporter can be inhibited by Atractyloside, can be isolated from a thistle
43
Q

What membrane transporters are involved in the synthesis of ATP?

A
  • Phosphate translocase
    • symporter of H+ and H2PO4-
    • this provides the phosphate needed for oxidative phosphorylation of ADP
  • ATP Synthase
    • an F-type ATPase formed of two functional domains- F0 and F1
    • F0 is a proton channel
      • it is oligomycin sensitive
    • F1 ​is an ATP synthase
44
Q

Summarise how ATP is synthesised by ATP synthase

A
  • F1 made of 5 subunits; the beta subunits have catalytic sites for ATP
  • the beta sites change their conformation
    • for ADP and Pi binding then
    • for binding to ATP tightly then
    • change to give active site low affinity for ATP (allows ATP to be released)
  • this is facilitated by the rotation of the gamma unit
45
Q

How does Brown adipose tissue generate heat?

A
  • has a high no. of mitochondria
  • mitochondria contain thermogenin- UCP-1
    • acts as an uncoupler
    • H+ is transported back into the matrix without synthesizing ATP
    • DNP is an exogenous example
  • important in newborns
46
Q

What is DNP- 2,4-dinitrophenol?

A
  • weak acid that crosses mitochondrial membrane with H+ ion, into the matrix
  • highly toxic to the liver
    • can cause respiratory acidosis and hyperthermia
47
Q

What are some distinct difference between the Nuclear and Mitochondrial genome?

A
  • mt has a higher gene density
  • mt doesn’t contain introns
  • has significantly higher % of coding DNA
  • exclusively maternal
  • not associated with histones
  • mutates faster due to more damage from ROS and less correcting of mt DNA
48
Q

How do defects in oxidative phosphorylation present themselves?

A
  • involve tissues most reliant on OXPHOS
  • occur later in life
  • progressive with age
  • show progressive enrichment in mutated mtDNA’s
49
Q

What are the two phenotypic/ variable penetrance that governs the presentation of a mt disease?

A
  • Threshold effect (homoplasmy and heteroplasmy of mt)
    • a certain amount of mutated or dysfunction mt is needed for the disease to be present
    • during cell division, the progenitor cell with heteroplasmy could divide to give normal or a diseased cell
  • Mt Genetic Bottleneck
    • if the mature oocyte has a high level of mutation
50
Q

Give 5 biochemical classifications of Mt myopathies

A

Defects of

  • Mitochondrial transport systems
    • ​CPT I and II ( can’t use certain fat for energy)
  • Substrate utilisation
    • ​Pyruvate Dehydrogenase Complex deficiency
    • Fatty acid oxidation defects
  • TCA cycle
    • ​Fumarase deficiency/ alpha-ketoglutarate dehydrogenase deficiency
  • OXPHOS coupling
    • ​Luft’s syndrome: hypermetabolism, heat intolerance, polydipsia without polyuria
  • Oxidative phosphorylation
    • ​deficiency in the Complexes I toV
51
Q

Give 4 key Mt Myopathies

A
  • Lebers Herideritary optic neuropathy: LHON
  • Myoclonus epilepsy with ragged fibre: MERRF
  • Mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes: MELAS
  • Kearns-Sayre syndrome: KSS
52
Q

Lebers hereditary optic neuropathy

Give more detail on LHON syndrome and its impact

A
  • SNP in mt change ND4
    • Arg to His in a polypeptide of Complex I
    • can also be an SNP in mt gene for cut b in complex III
  • there is a defect in é transport from NADH to ubiquinone
    • not enough ATP produced in mt for neurons
  • results in a damaged optic nerve
53
Q

Myoclonus epilepsy with ragged-red fibre

Give more detail on MERRF syndrome and its effect

A
  • point mutation in mt gene encoding tRNALys
    • disrupts the synthesis of proteins essential for OXPHOS
    • in 80% of cases occurs at position 8344 in the mt genome
  • effects other genes, mtTK, mtTL1, mtTH, mtTF
  • skeletal muscles fibres are abnormally shaped
  • the ragged-red fibres are clumps of defective mitochondria that accumulate in aerobic skeletal muscle fibres
    • appear red when stained with Gomeri modified Trichrome
54
Q

Mitochondrial encephalomyopathy

Give more detail on MELAS syndrome and its effects

A
  • effects the mtND5 gene - complex I
    • also affects mtTH, mtTL1 and mtTV - all involved with tRNA
  • mainly affects the brain/SNF and skeletal muscle
  • symptoms appear in childhood
    • lactic acidosis
    • stroke-like episodes
    • seizures –> loss of vision
    • movement difficulties + myoclonus
    • dementia
55
Q

Kearns-Sayre syndrome

Give more detail on KSS and its effects

A
  • from a 5kb deletion of the mt genome
  • onset before age 20
  • short stature and often have multiple endocrinopathies including diabetes
  • Symptoms: dementia and retinitis pigmentosa
    • lactic acidosis
    • heart conduction defects
    • raised cerebrospinal fluid protein content
56
Q

What are some treatments of mt myopathies and how are they diagnosed?

A
  • Diagnosed
    • biochemical tests
    • histology
    • genetic testing
  • Treatment and Prognosis
    • prognosis is variable depends on the individual’s metabolism
    • occupational/physical therapy- help with muscle movement
    • vitamin therapies: riboflavin, creatine, CoQ, C, K, carnitine

there is no specific treatment apart from the development of genetic strategies

104: Theme 2 (7 decks)

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