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Year 3 - Chemistry > Options: Natural Products > Flashcards

Options: Natural Products Flashcards

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1
Q

What are features of primary metabolic processes?

A

Processes esssential to life
They are conserved across species

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2
Q

What are some examples of primary metabolic processes?

A

Formation of: carbohydrates, acetly coenzyme A, amino acids, nucleotides, etc

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3
Q

What is a secondary metabolic process?

A

Processes non-essential to life
Change species to species

Rel small # of starting materials and wide range of products

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4
Q

What is acetyl coenzyme A and mevalonic produced from?

A

Derived from acetate

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5
Q

What can acetyl coenzyme A be used to make?

A

2ndary metabolism process:
Fatty acids
Prostaglandins
Polyketides
Phenols

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6
Q

What can be made from mevalonic acid?

A

2ndary metabolism process:
Terpenes
Steroids

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7
Q

What can amino acids be used for in 2ndary metabolism?

A

Producing alkaloids

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8
Q

Define enzymes

A

Biological catalysts (not used up)
Dictates substrate selectivity, chemio, regio and stereoselectivity of the reaction

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9
Q

Define cofactors

A

Biochemical reagents which contain reactive functional group and groups for recognition/binding to the enzyme

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10
Q

What are the classes of metabolic enzymes?

A

Oxidoreductases - redox reactions
Transferases - functional group transfers
Hydrolases - bond hydrolysis
Lyases - elim reactions, and ring formation
Isomerases - isomerisation reactions
Ligases - condensation reactions

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11
Q

What is NADPH?

A

Hydride donor

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12
Q

What is NAD+?

A

Hydride acceptor (deprotonated form of NADH)

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13
Q

How is NADH synthesised?

A

Hantsch pyridine synthesis

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14
Q

What is the mechanism of Hantzsch pyridine synthesis?

A
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15
Q

What occurs to Fe(II) and O2?

A
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16
Q

How does Fe(II) and O2 react with an alkene (and benzene)?

A

Epoxidation

Benzene - acid to rearomatise to phenol, and can do twice

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17
Q

How is Fe(II) and O2 used for benzylic oxidation?

A

Occurs as activated C-H
Reaction stops here - with KMnO4 would carry on

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18
Q

What is SAM, s-adenosyl methionine?

A

Methylating agent equivalent to MeI

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19
Q

How is SAM made?

A

Methionine and ATP -> SAM + triphosphate + nucleoside

S attacks C on ATP via an Sn2 style
Then reacts via Sn2

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20
Q

How can you alkylate an alcohol biochemically?

A

ATP then Nucleophillic C or S

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21
Q

How can you perform acylation biochemically?

A
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22
Q

What is the stability of esters and thioesters?

A

Esters favoured thermodynamically

As S 3p has poorer overlap

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23
Q

What is the pKa of esters compared to esters?

A

Thioester pKa is around that of anhydride rather than ester

Means enolate chem of thioester closer to ketone

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24
Q

How are polyketides formed?

A

Enolate chemistry which occurs as produces more stable anion

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25
Q

What are fatty acids?

A
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26
Q

What is required for fatty acid synthesis?

A

CO2 required but those C are not incorporated into fatty acids
Malonyl coenzyme A is starting material

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27
Q

How is malonyl coenzyme A made in step 1 of fatty acid synthesis?

A

Uses biotin - which is a CO2 carrier

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28
Q

What are the steps in fatty acid synthesis?

A

1) Malonyl coenzyme A synthesised
2) form a β-unsaturated thioester
3) Form an ester

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29
Q

How does a form a β-unsaturated thioester form in fatty acid synthesis?
(step 2)

A
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30
Q

How does a form fatty acids from β-unsaturated thioesters?

A
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31
Q

What is the complex in fatty acid synthase?

A

All enzymes are in the same complex

Also uses acyl carrier proteins - shuttles around complex to enzyme reaction site

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32
Q

How are fatty acids unsaturated or saturated?

A

Unsaturation by a disulfide

Saturation by O2

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33
Q

What are the uses of prostaglandins and leukotrienes?

A

Sensing pain
Inflammation

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34
Q

What are prostaglandins made from?

A

Fatty acids
which themselves are made from acetyl CoA as above

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35
Q

What enzyme is used for prostaglandin synthesis and how is it inhibitied?

A

Cyclooxygenase (COX) - Fe dependent enzyme

Inhibited by drugs such as ibuprofen, which prevents pain/inflammation

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36
Q

What is arachidonic acid?

A

Fatty acid commonly used in synthesis of prostaglandin or leukotrienes

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37
Q

How are prostaglandins synthesised from arachidonic acid?

A

Cyclooxygenase (COX) dependent
First radical is doubly-stabilised as it is a diene

38
Q

What can be done to modify prostaglandins?

A

Use different reagents:
NADH cleaves O-O bond in ring to give OH
Selectively reduce terminal peroxide then treat with acid

39
Q

How are leukotrienes synthesised from arachidonic acid?

A

5-lipoxygenase enzyme and O2

40
Q

What are polyketides used for?

A

Synthesis of polyaromatics

41
Q

What is an example of mechanism for tetraketides reacting to form an aromatic?

A

Can have deprotonation at different areas

42
Q

How can you introduce diversity to ketides?

A

Branching - Base then SAM for methylation

Decarboxylation after thioester to carboxylic acid

43
Q

What is a common side-reaction in polyaromat synthesis?

A

If NADH to produce aldehyde can also have intra attack

44
Q

How can oxidase be used when making polyaromats?

A
45
Q

How can dioxygenase be used in polyaromat synthesis?

A
46
Q

When are partially saturated polyketides made?

A

Made from interrupted sequence during their synthesis

47
Q

How can you make a partially saturated polyketide?

A

Where:
KS = ketosynthase - extends by one ketide
KR = ketoreductase - reduces non thio carbonyl
DH = dehydratase - alcohol to alkene
ER = enoyl reductase - enone to carbonyl

48
Q

What is isoprene?

A

Thought to be base unit of isoprenoids and terpenes

49
Q

How can you create an isoprene equivalent?

A

Acetyl coenzy A -> R-mevalonic acid -> isoprene equivalent

50
Q

What is R-mevalonic acid?

A

This is intermediate to producing an isoprene equivalent

51
Q

How do you synthesise mevalonic acid from acetyl coenzyme?

A

1)Acetyl CoA + 2x Acetacetyl CoA then hydrolysis

2)Reduction with NADH and H+

52
Q

How is mevalonic acid reacted to make an isoprene equivalent?

A

React OH with 2xATP (primary then teriary)

53
Q

How does isopentyl pyrophosphate react in acid?

A

This generally occurs before reacts in biological synthesis

54
Q

What is the reactivity of isopentyl pyrophosphate with nuc?

A
55
Q

How are terpenes made from isopentyl pyrophosphate?

A

This can go on to produce longer terpenes (all E)
Then will intramolec react

56
Q

How are terpenes form from intermediate?

A

Intramolec reaction

57
Q

How are bridged cyclic systems made from terpenes?

A
58
Q

How does the wagner-meerwein shift occur in terpene shift to give diversity?

A

Always look at putting the +ve charge on more sub atom

59
Q

How can terpenes be modified with COX?

A

Replaces an alkyl H with OH
Can then be oxygenated via NAD+ to carbonyl

60
Q

What is squalene?

A

Intermediate in cholesterol synthesis

61
Q

How is squalene synthesised?

A

Produce 2x farnesyl pyrophosphate which can then couple with eachother

62
Q

How do 2x farnesyl pyrophosphates couple?

A
63
Q

How does squalene convert to make a steroid?

A

Use COX to form epoxide then draw chairs (next to eachother) and do a chain alkene process

Then use Enz to abstract protn and sequential 1,2- C-H/C-Me migrations

64
Q

What does a desaturase enzyme do?

A

Forms an alkene from alkyl in a cholesterol molecule

Abstracts H2

65
Q

What does vitamin D mean?

A

Group of structurally related secosteroids

They regulate absorption of minerals such as Ca2+ and Mg2+

66
Q

How can you make a vitamin D compound?

A

UV (like sunlight on skin!)

Causes 6π photochem electrocyclic ring opening

67
Q

What are alkaloids?

A

N-containing 2° metabolite (non-peptidic/nucleoside)

Mostly derived from α-amino acids
Types: aliphatic, aromatic, indole alkaloids

68
Q

What are examples of aliphatic alkaloids?

A
69
Q

How are amino acids biosynthesised conceptually?

A

α-ketocarboxylate to α-amino acid
Amine transfer using pyridoxamine / pyridoxal phosphate

Uses: aminotransferase, glutamic acid

70
Q

What is the mechanism for amino acid synthesis?

A

This is in wrong order

71
Q

How can you use pyridoxal phosphate to racemise an amino acid?

A
72
Q

How is pyridoxal phosphate used as a cofactor?

A

Acts as an aldehyde
N can attack to form an imine
Then reacts via imine chemistry

73
Q

What reactions use pyridoxal phosphate as a cofactor?

A
  • C-C formation
  • Sub at β-position at α- amino acids
  • Internal redox reactions
  • Oxn of primary amine
74
Q

How do you perform a decarboxylation of an amino acid?

A
75
Q

How is proline synthesised?

A
76
Q

How is orthinine synthesised from glutamate?

A
77
Q

What is the urea cycle?

A
78
Q

How is α-ketoglutarate?

A
79
Q

How is lysine synthesised?

A
80
Q

What is the overview of glycolysis?

A

Glucose to pyruvate
Produces ATP, CO2, and H2

81
Q

What occurs in glycolysis?

A
82
Q

What is thiamine pyrophosphate (TPP)?

A

Acts like a cyanide:
Good nuc
Stabilises adj -ve charge
Good LG

83
Q

How can you use TPP for a reaction?

A
84
Q

What is the mech of using TPP?

A
85
Q

How does an amide with an aromatic system react with POCl3?

A
86
Q

How can an aryl group react with an imine?

A
87
Q

What technique can be used to make complex alkaloids?

A

Oxidative radical coupling

Includes ortho/para or ortho/ortho coupling

88
Q

What is the mechanism of oxidative radical coupling when ortho/para?

A
89
Q

What is the mechanism of oxidative radical coupling when ortho/ortho?

A
90
Q

What does this reagent do?

A

Reacts with more e- rich OH (out of the ones on the ring)

Gives RO-I(Ph)-OCOCF3

91
Q

What is the polonovski reaction?

A

Year 3 - Chemistry (12 decks)

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