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MBB266 > Staniforth (Biosynthesis and metabolism) > Flashcards

Staniforth (Biosynthesis and metabolism) Flashcards

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1
Q

Why did evo of CO2 (decarboxylation) give strong thermodynamic pull to reactions?

A
  • v stable
  • easily escapes site of reaction (as gas/soluble bicarb)
  • more products than reactants (-ΔG)
    (R-COOH RH + CO2)
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2
Q

How does carbon enter metabolism?

A
  • photosynthesis
  • carboxylations
    eg. pyruvate + CO2 –> oxaloacetate
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3
Q

How does hydrogen enter metabolism?

A
  • H2O
  • NH4
  • H2 (g)
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4
Q

How does oxygen enter metabolism?

A
  • H2O
  • CO2
  • molecular oxygen reactions
  • Phe + O2 –> Tyr (+ΔG)
    = biosynthetic reaction as uses NADPH, not NADP
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5
Q

Where is S found in cell?

A
  • SH = high energy thioesters
  • Fe-S proteins = redox centres
  • SH groups important for protein folding
  • energy store
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6
Q

Why is acetyl CoA high energy?

A
  • great bond donor and easily separated to donate CoA group
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7
Q

Why are S proteins so common?

A
  • pyrites used in primitive Earth instead of NADH –> NAD+
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8
Q

How does S enter metabolism?

A
  • MOs/plants get from H2S

- higher organisms get from diet, eg. Met

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9
Q

What are the advantages of using S?

A
  • S-S bonds strong but form and break under mild conditions (so more flexible)
  • S binds to Fe
  • thioesters have less resonance stabilisation than O esters –> carry more G
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10
Q

How is Ser used to get Cys?

A
  • Ser activated by acetyl CoA

- captures S from H2S to give Cys

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11
Q

How does nitrogen enter metabolism?

A
  • N2 (g) v stable = N fixation by nitrogenase
  • NH3 quite stable = by glutamate deHase
  • glutamate synthase
  • glutamine synthetase
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12
Q

What is the importance of nitrogen in metabolism?

A
  • forms H bonds and Schiff base links
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13
Q

How does P enter metabolism?

A
  • naturally oxidises to phosphate under atmospheric conditions
  • phosphate used directly by cell
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14
Q

What is the difference between 1° and 2°metabolic pathways?

A

1°

  • basic housekeeping functions
  • in essentially all cells
  • largely constitutive

2°

  • specialised functions
  • in all differentiated cells
  • inducible
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15
Q

What are the functions of glycolysis?

A
  • ATP and NADH prod

- intermediates for biosynthesis

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16
Q

What is the location of glycolysis?

A
  • cytosol
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17
Q

What is the overall reaction of glycolysis and pentose phosphate pathway?

A
  • glucose –> pyruvate
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18
Q

When is glycolysis used, and when is phosphate pentose pathway used?

A
  • glycolysis if cell needs energy

- PPP if cell needs biosynthesis

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19
Q

What are the functions of pentose phosphate pathway?

A
  • gen C5 sugars and NADPH for biosynthesis
  • breakdown route for C5 sugars
  • other intermediates for biosynthesis
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20
Q

What is the location of pentose phosphate pathway?

A
  • cytosol
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21
Q

What is the overall reaction of Link Reaction?

A
  • pyruvate —-pyruvate deHase—> acetyl CoA + CO2 + NADH
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22
Q

Is Link reaction favourable, and why?

A
  • v favourable

- decarboxylation

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23
Q

What are the functions of the Link Reaction?

A
  • processes pyruvate for KC
  • source of acetyl CoA
  • NADH prod
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24
Q

What is the location of the Link Reaction?

A
  • mito
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25
How Krebs Cycle discovered to be a cycle?
- measured resp in muscle tissues - added succinate and lots more C prod than what was added - ∴ cycle w/ catalytic property
26
What are the functions of Krebs Cycle?
- NADH and GTP prod | - gen intermediates for biosynthesis
27
What is the location of the Krebs Cycle?
- mito
28
How does ATP prod by Krebs Cycle compare to glycolysis?
- 24 v 2
29
What is a top up (anaplerotic mechanism) for Krebs Cycle?
- pyruvate + CO2 + ATP + H2O --> oxaloacetate + ADP
30
Why is a cycle a good design for a precursor supply system?
- extra supply of any intermediate can top up cycle
31
What are the functions of mito e- transport system?
- gen ATP (via NADH and FADH2) and GTP | - maintaining redox balance (NADH-->NAD+)
32
What reaction occurs during β-ox of FAs?
- FAs --> acetyl CoA | - NADH and FADH2 prod
33
What are the functions of β-ox of FAs?
- extracting energy from lipid stores | - gen 2C units for biosynthesis
34
What is gluconeogenesis?
- opp of glycolysis | - biosynthesis of sugars from non-carb prescursors
35
What is the overall reaction of gluconeogenesis?
- pyruvate, AAs --> sugar
36
What is the function of gluconeogenesis?
- sugar supply when glucose scarce
37
What are the locations of gluconeogenesis?
- mito and cytosol | - mainly liver, some in kidney
38
What are the 3 methods for control of biosynthetic pathways?
- isoenzymes - single enzyme cumulative control - single enzyme concerted control
39
How can isoenzymes be used to control biosynthetic pathways?
- several enzymes doing same job, w/ small diff, so 1 can be inactivated but not others
40
What is an example of a pathway using isoenzymes?
- amino acid biosynthesis - 3 diff asportkinases in E. Coli for conversion of aspartic acid to aspartyl phosphate - same aspartokinase domain, but slightly diff regulatory domain - 1 is not inhibited, 1 inhibited by Thr and 1 inhibited by Lys
41
How can a single enzyme with cumulative control be used to control biosynthetic pathways?
- eg. glutamine synthetase - 1 product has inhibitory activity - next has more until enzyme totally inhibited * DIAGRAM*
42
How can a single enzyme with concerted control be used to control biosynthetic pathways?
- eg. lysine biosynthesis - each product alone has no inhibitory activity - combo of products gives inhibitory activity * DIAGRAM*
43
What is the rate determining step?
- slowest step
44
What is the committed step?
- means reaction continues - relax control and get end product - don't if heighten it - not necessarily slowest
45
Why is distributive control of pathways a poss?
- prob over simplification to say cellular control of pathways occurs directly by variations in rate of indiv enzymes
46
What is the distributive control hypothesis?
- flux through a pathway is a system property rather than simply property of indiv control enzymes
47
What is flux?
- no. molecules being transformed per unit time | - not equal to conc
48
What is the equation to calc flux coefficient (C)?
- (steady state flux/steady state flux) / [enz]/[enz]
49
What diff values of flux coefficient (C) do enzymes have at diff points in pathway, and what does this contradict?
- early enzymes have low C values - later enzymes have high C values - contradicts traditional role of allosteric control
50
How do you do metabolic flux analysis?
- identify enzymes involved in pathway - map levels of as many intermediates as poss ('metabolome') - investigate effect of increase or decrease in amount/activity of specific enzymes - work out contribution of each enzyme to overall flux
51
What is the metabolome?
- quantitative complement of all low mol weight molecules present in cell under given conditions
52
What is the greatest implication of distributive control hypothesis?
- for biotechnologists | - need to decide which enzymes to increase/improve to result in enhanced yields of useful products
53
In the pathway A ---enz 1--> B ---enz 2--> C ---enz 3--> D what effect would increasing levels of enz 2 have?
- increase rate of B --> C - decrease B - increase C - not as high and as an immediate effect as would expect, as enz 1 and 3 still have impact
54
How do you increase flux through pathway?
- increase amount of single enzyme rarely increases flux - increasing several enzymes does - nature usually increases all enzymes in pathway, eg. lac operon
55
Is pathway of biosynthesis distinct from pathway of degradation?
- usually
56
What is the basic principle of group carriers/donors?
* DIAGRAM* - molecule of B loaded onto carrier and activates it - carriers energetically unstable when loaded so -ΔG to donate group - loading generally req energy
57
What are the major group carriers for biosynthesis?
- C1 = tetrahydrofolate - C1-methyl = s-methyladenosine - C1-carboxyl = biotin - C2 = acetyl CoA - C3 = PEP - C5 = isopentenyl pyrophosphate - amino = Gln/Glu - sulfur = Cys - sugar = nucleosidediphosphates - complex (eg. C-C-N) = eg. Gly
58
Why is biotin a good carrier molecule?
- preferable for CO2 to leave as lots of Os close together
59
How does biotin donate its COO group?
- ATP + bicarb --> carboxyphosphate | - carboxyphosphate wants to lose phosphate, cat addition of COO group to biotin (forms carboxybiotin enzyme)
60
What is an example of COO addition via biotin?
- pyruvate --> oxaloacetate - cat by pyruvate carboxylase - biotin-COOH donates COOH - KC anaplerotic reaction
61
What group does tetrahydrofolate contains many copies of?
- Glu
62
Can C1 be carried in a variety of oxidation states?
- yes
63
What is the role of FH4 in the biosynthesis of dTMP?
- donates methyl group (unusual) - during donation, FH4 converted to FH2 - NADPH needed to reconvert FH4 (energy input) - ultimate source of methyl group is Ser
64
What is the most common methyl group carrier?
- S-adenosyl methionine (SAM)
65
How does SAM donate its methyl group?
- activation req ATP - CH3 activated by S+ - Ser ultimate source of methyl groups (via FH4)
66
Why is methyl group on SAM a good leaving group?
- S+ next to it tries to grab e-s
67
What is the outline of SAM structure?
- S+ w/ single bond to adenosine, CH3 and Met
68
What is an example of C2 donation?
- FA biosynthesis
69
Why does phosphoenolpyruvate have no carrier (C3 units)?
- in built energy source
70
Why is phosphoenolpyruvate (C3) a good donor?
- -ve groups attached to each other | - not good sterically so -ΔG to get rid of repulsion
71
How does isopentenyl pyrophosphate donate C5 group?
- mevalonic acid made up of 3 acetyl CoAs - CO2 lost forming IPP, pulls reaction forward - IPP v reactive, has high free energy of reaction - reactions occur leading to highly reactive carbonium ion
72
How are NH2 groups donated?
- Gln --> Glu +NH2 - uses ATP - no activated carrier - only R group NH2 donated
73
What various types of C1 unit can be carried on FH4?
- methanol (CH3-OH) - formaldehyde (H2C=O) - formic acid (OH-HC=O)
74
What is the diff between purine and pyrimidine skeletons?
- purine 2 ring | * DIAGRAMS*
75
What is phosphoribosyl pyrophosphate important for?
- allosteric control and end product inhibition as control of biosynthesis often involves 1st/2nd step
76
What is phosphoribosyl pyrophosphate?
- high active form of ribose
77
What are the 2 phases of purine biosynthesis?
- activation of O by phosphorylation | - nucleophile attacks activated C
78
What kind of donor can Asp function as?
- NH2
79
What are the origin of all atoms in purine skeleton?
- N from Asp - N from Gln - NH from Gln - CCN from Gly - 2x CH from FH4 - CH from CO2
80
What is the core pathway in purine biosynthesis?
- ribose-5-P --> PRPP --> phosphoribosylamine --> IMP
81
What are the processing reactions in purine biosynthesis?
- IMP --> AMP | - IMP --> GMP
82
Why is GTP used in processing of IMP to other nucleotides?
- if making ATP, makes sense to use diff nt in its biosynthesis
83
Why is deoxyribose wanted in DNA instead of ribose?
- more stable | - so can survive longer than RNA
84
What is the overall control of purine nt biosynthesis?
- overall control/end product feedback - balancing levels of ATP/GTP - balancing levels of purines/pyrimidines - balancing levels ribose vs deoxyribose - not clear if cumulative or concerted but def not isoenzymes
85
Why is control of purine nt biosynthesis necessary?
- avoid wastage and holding anything back
86
How is the biosynthesis of purine nts balanced?
- end products (ATP/GTP) are co-reactants in opp branch for conversion of IMP
87
What is tetrahydrofolate used for, and why does it have such serious side effects?
- widely used drug in chemo | - side effects as affects DNA and RNA synthesis
88
What is Ki, and what do the values mean?
- inhibition constant = how tightly enzyme bound | - <1 means need hardly any and it binds, so good comp inhibitor
89
How can fluorouracil and methotrexate be used in cancer chemo?
- fluorouracil = fluorinated analog of dUMP, inhibitor - only works w/ pyrimidine nts (not purine analogs) - ring assembled, then ribose-P attached - methotrexate kills all rapidly dividing cells (inc bone marrow, hair follicles) --> Ki < 1nM
90
How is chirality of Cα established?
- transamination reaction using pyridoxal phosphate
91
What are the 3 enzymes of amination?
- glutamate deHase - glutamate synthase - glutamine synthetase
92
Why is double bond formation important in AA formation?
- prevents rotation --> planar
93
What is Schiff base formation?
- NH2 + -CHO
94
Why is Schiff base formation important in establishing chirality?
- geometry of enzyme ensures H+ added from specific side
95
What are the metabolic families of AAs? | need to know 1 eg.
- oxaloacetate - PEP - ribose-5-P - pyruvate - 3-phosphoglycerate - α-ketoglutarate
96
How are AAs classified into families?
- according to their biosynthetic precursor
97
What are the general principles of AA biosynthesis?
- intermediate of glycolysis/PPP/KC --> req side chain assembled on α-keto acid --> NH2 group added by transamination
98
What is the mechanism of glutamate deHase?
Transamination: 1) binding of PLP to enzyme - binds reversibly 2) exchange - Schiff base formation is reversible 3) transfer of -NH2 to PLP - addition of water 4) 2nd substrate - loss of water - Schiff base formed 5) Schiff base linkage exchange w/ enzyme - AA has effectively exchanged R group
99
How is transamination poss?
- exchange of amino groups freely reversible - AAs form "pool" to freely interchange - similar amount of each AA until 1 req - not great for control, but good for supply
100
What are the contrasting roles of Glu and Gln in biosynthesis of NH2 containing molecules?
- Glu has COOH / Gln has CONH2 - α-amino group of most AAs from Glu - Gln major donor of NH2 groups in biosynthesis
101
How is Ser biosynthesised?
- from 3-phosphoglycerate | - req NAD, Glu and H2O
102
How does KM control amination?
- α-oxoglutarate --> glutamate - high KM at high [NH3] = use of NH3 and NADH - low KM at low [NH3] = use of NH3, ATP and NADPH
103
What method of pathway control is used for end product inhibition on glutamine synthetase?
- cumulative inhibition
104
What are the 2 forms of glutamine synthetase interconverted at adenylyl transferase, in the control of glutamine synthetase?
* DIAGRAM* - ATP used to add AMP group - adenylyl transferase has dual specificity, specifically changed by protein
105
What are the 2 forms of P protein in the control of glutamine synthetase?
- adenylating form deadenylating form (addition of UMP) - cat by uridyl transferase - reverse reaction spontaneous
106
What is the role of deadenylating form of P protein?
- turns glutamine synthetase back to active form
107
How is uridyl transferase under allosteric control?
- glutamine --> uridyl transferase
108
What is the significance of control of uridyl transferase?
- reaction important threshold in N reactions, so has stringent control - mini amplification cascade?

MBB266 (7 decks)

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