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Biostructures energetics and synthesis > Williamson - Metabolism > Flashcards

Williamson - Metabolism Flashcards

1
Q

what is catabolism

A

making energy, oxidative

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2
Q

what is anabolism

A

using energy to make things, reductive

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3
Q

what is produced/required in catabolism vs anabolism

A

catabolism = produces NADH
anabolism = requires NADPH
eg. glycolysis and gluconeogenesis
- makes separate

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4
Q

how much ATP can be made from NADH

A

3 ATP

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5
Q

how much ATP can be made from FADH2

A

2 ATP

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6
Q

why are reactions which liberate CO2 very energetically favourable

A

CO2 is very stable (lower free energy than reactants)
it easily escapes from the reaction site (law of mass action)
a reaction which produces CO2 has more molecules on the right (higher entropy)

therefore it is a useful committed step eg. in the link pyruvate to acetyl CoA

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7
Q

redox status

A

must be balanced if something is getting oxidised something else must be reduced

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8
Q

is anabolism mainly reduction or oxidation

A

reduction
NADPH is used to reduce substrates

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9
Q

what is metabolic flux

A

where did the atoms (eg. C) come from and where did they go

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10
Q

where is our carbon from

A

food, ultimately photosynthesis - fixing CO2
energy for this coming from the sun

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11
Q

what is an anaplerotic reaction

A

used to top up an atom (eg. carbon) in a biosynthetic pathway
ana - add
plero - more

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12
Q

how can we fix carbon

A

pyruvate + CO2 –> oxaloacetate
using ATP, and pyruvate carboxylase

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13
Q

what is a threshold enzyme + examples

A

enzymes which bring key elements into biosynthetic pathways
eg. pyruvate carboxylase and glutamate dehydrogenase

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14
Q

characteristics of a threshold enzyme

A
  • tightly regulated
  • non-constitutive
  • high affinity for substrate
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15
Q

what is the carrier for COO

A

biotin vitamin b7

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16
Q

what is the carrier for C1 (methyl)

A

s-adenosyl methionine

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17
Q

what is the carrier for C1 (CH or CH2)

A

folic acid

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18
Q

what is the carrier for C5

A

isopentenyl pyrophosphate

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19
Q

what is the carrier NH2

A

glutamine

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20
Q

what is the carrier C2

A

Coenzyme A, from vitamin B5
has a sulphur making it more reactive

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21
Q

what is a vitamin

A

essential molecules we cannot make ourselves
often carriers

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22
Q

what role does biotin play in the Krebs

A

it is the carrier of COO in the anaplerotic reaction of pyruvate to oxaloacetate to top up carbon in the Krebs

23
Q

how does a folate molecule bind CH2 or CH

A

with N “claw” - 2 nitrogens surround it
folate can change it oxidation states to carry the 2 forms of carbon

24
Q

where does the methyl group bind to s-adenosylmethionine

A

the sulphur of the methionine
the adenosine is a handle

25
Q

why is s-adenosylmethionine important

A

it carries methyl groups which are important in epigenetics
- DNA
- and histones
and important for the ripening of fruit

26
Q

what is an example of C2 donation

A

link reaction
fatty acid biosynthesis

27
Q

how are C5 units made

A

6 units of acetyl CoA
- 1C removed as CO2

28
Q

what are C5 units used for

A

steroids
eg. terpenes - plant signals also smells eg. menthol
retinol
haem and chlorophyll

29
Q

what is glutamate used for

A

main carrier of nitrogen
nucleic bases

30
Q

what is the pentose phosphate pathway for

A

interchanging different sugars (different lengths of Cs)
making biosynthetic intermediates
especially making ribose

31
Q

what human cell can only do glycolysis

A

RBCs

32
Q

what is a ketone body

A

fats which are soluble in water - can cross BBB

33
Q

how does pyruvate become alanine

A

a transamination reaction (swapping a C double bond O for an C-NH2
done by alanine transaminase

34
Q

what are some differences between the pentose phosphate pathway and glycolysis

A

it uses NADPH (P = hint to biosynthesis)
it releases a CO2 at the start - control

35
Q

what are the roles of acetyl CoA

A

making energy
biosynthesis
synthesising fatty acids

36
Q

once carbon atoms have gone from pyruvate to acetyl CoA can they go back?

A

no

37
Q

what krebs intermediate is used to make fatty acids

A

citrate (6C)

38
Q

what krebs intermediate is used to make amino acids

A

α-ketoglutarate (5C) and oxaloacetate (4C)

39
Q

what krebs intermediate is used to make porphyrins (haem, chlorophyll)

A

succinyl CoA (4C)

40
Q

does the krebs cycle go backwards

A

yes especially in photosynthetic bacteria and plants for biosynthesis

41
Q

what is the breakdown of fatty acids

A

beta-oxidation
because you chop off 2 carbons at a time
the first being -CH2-COOH = acetyl CoA
same enzyme for different length substrates - fatty acid oxidase

42
Q

can fats be converted to sugars

A

not directly, only the glycerol headgroup which can feed into gluconeogenesis

43
Q

how are fatty acids synthesised

A

opposite of breakdown
same enzyme adds 2 carbons to the chain each time

44
Q

how is nitrogen moving around compounds in AA synthesis

A

moved around from glutamate using transamination

45
Q

what does nucleotide biosynthesis use as a committed step and why?

A

ATP –> AMP
this is a big free energy change
favourable and less likely to go backwards
= important to get right

46
Q

what are the four ways metabolism can be controlled

A
  1. isozymes
  2. cumulative regulation of one enzyme by multiple products/substrates
  3. expressional regulation
  4. change in [substrate] - metabolic flux
47
Q

what does ATP inhibit

A

energetic pathways

48
Q

what does ADP inhibit

A

biosynthetic pathways

49
Q

what is enzyme multiplicity (isozymes)

A

having multiple different isozymes with different allosteric modulators
eg. lactate dehydrogenase
different components H4 to M4

50
Q

what is cumulative control of a single enzyme

A

when one enzyme is regulated by multiple different substrates or products
often includes kinases which temporarily phosphorylate an enzyme making it inactive
eg. glycogen phosphorylase

51
Q

what is expression control of an enzyme

A

presence of a substrate removes a repressor eg. lac operon
or presence of a product causes a repressor to bind

52
Q

transamination what AA forms alpha-ketoglutarate

A

glutamine

53
Q

transamination what AA forms oxaloacetate

A

arginine

Biostructures energetics and synthesis (4 decks)

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