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Biological Chemistry > organic chemistry > Flashcards

organic chemistry Flashcards

1
Q

What is a primary alcohol

A

the carbon the OH is bonded to is attached to one carbon (secondary - 2)(tertiary - 3)

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2
Q

Which alcohols are soluble

A

C1 - C3 (soluble due to H bond with OH), as the chain length increases more hydrophobic properties are introduced, decreasing solubility

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3
Q

Why do alcohols have relatively high boiling points

A

hydrogen bonding in the OH, so more OH groups the higher the BP

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4
Q

Why does a longer chain have a higher boiling point

A

larger molecule so has stronger forces

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5
Q

How is glycerol made and what are its uses

A

by product of soap and biodiesel manufacture. Used as moisturiser, sweetener etc…

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6
Q

1,2 ethandiol uses and hazards

A

antifreeze. Ingestion can lead to death by alcohol dehydrogenase, to treat add ethanol

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7
Q

Oxidation of alcohols

A

primary alcohol - aldehyde then carboxylic acid. Secondary alcohol - ketone. Tertiary does not oxidise.

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8
Q

Alcohols acting as an acid

A

the longer the chain, the weaker the acid. Reacts with alkali metals to release hydrogen and an anion (alkoxide)

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9
Q

What are alkoxides

A

strong bases that are used in organic synthesis when strong base required in non aqueous solution

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10
Q

How can alcohols act as a base

A

in the presence of a strong acid by accepting a proton to form an oxonium ion

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11
Q

What reactions do primary oxonium ions undergo

A

do not lose water to form primary carbocations (too unstable) so undergo elimination or can be directly attacked by nucleophiles (SN2)

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12
Q

What is the ether functional group

A

R-O-R

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13
Q

Ether as a polar molecule

A

More polar than alkanes due to the presence of oxygen but less than alcohols as there is no hydrogen attached to the oxygen

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14
Q

Hydrogen bonding in ether molecules

A

exists between water and ether but not between ether molecules

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15
Q

Chemical features of ethers

A

little reactivity so are normally used as solvents. Has a low boiling point

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16
Q

How to name an ether

A

For the shorter hydrocarbon chain, change -yl to -oxy

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17
Q

Hydrogen bonding in amines

A

exists between amines and water

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18
Q

What is a homologous series

A

successive compounds that differ by CnH2n

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19
Q

Where do alkanes appear in biology

A

animal pheromones, plant waxy cuticle and floral scents

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20
Q

What is an alkane

A

straight or branched hydrocarbons with only single covalent bonds between the carbons

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21
Q

What is an isomer

A

when 2 molecules have the same molecular formula but different 3D structure

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22
Q

What is a constitutional (structural) isomer

A

when molecular formulas are the same but arrangements of atoms differ

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23
Q

Why do branched alkanes have a lower boiling point

A

because they have a smaller surface area so don’t pack as well together, leading to fewer intermolecular interactions

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24
Q

What is free rotation

A

occurs around single bonds so alkanes are constantly moving. Creates conformation isomers

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25
Q

What is an eclipsed conformation isomer

A

When 2 of the atoms are closer together

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26
Q

What is a staggered conformational isomer

A

Atoms are the furthest away from each other

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27
Q

What is conformational isomerization

A

stereoisomerisation where isomers are formed by rotating around a single bond

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28
Q

Combustion of alkanes

A

results in CO2 and H2O

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29
Q

Cracking of alkanes

A

Breakdown of larger alkanes into smaller alkanes (smaller molecules are more useful)

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30
Q

dehydrogenation of alkanes

A

removal of H2 from an unsaturated hydrocarbon

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31
Q

Halogenation of alkanes

A

replacing a hydrogen with a halogen (free radical substitution - homolytic fission)

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32
Q

Which carbon is the most reactive

A

tertiary is the most then secondary and primary is the least reactive

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33
Q

Radicals being stabalized by hyperconjugation

A

As the radical forms the carbon center transforms from sp3 hybidized into sp2 hybridized. Delocalization of the bonding electrons from carbon next door by overlap with partly filled p orbital. Net stabilizing effect (less energy required to generate the radicals)

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34
Q

How many bonding pairs do primary, secondary and tertiary carbons need to stabalize

A

primary - 1, secondary - 2, tertiary - 3. Tertiary is the most stable (electron transducing effect)

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35
Q

What is the bonding in alkenes

A

sigma bond (sp2 from hybridisation) pi bond (overlap of p orbitals)

36
Q

What is a constitutional (structural) isomer

A

same molecular formula but different binding patterns and atomic organisations

37
Q

What is a geometric isomer

A

atoms arranged in the same order, but spatial arrangement differs

38
Q

What is a Z isomer

A

2 groups with highest priorities are on the same side

39
Q

What is an E isomer

A

2 groups with highest priorities are on opposite side

40
Q

What causes geometric isomers not to occur

A

if 2 identical groups are attached to the carbon

41
Q

cis/trans isomers in vision

A

11-cis-retinal derived from vitamin A combines with proteins (opsins) to form visual pigment Rhodopsin. Conversion triggers a cascade of events the brain interprets as seeing

42
Q

cis/trans isomers and fatty acids

A

most natural fatty acids are cis isomers, during cooking converted to trans isomers. Trans fatty acids can disrupt normal fatty acid processing increasing risk of stroke and heart attack

43
Q

Reactivity of double bonds

A

pi bond creates a high electron density above and below C=C making them suseptible to electrophillic attack. Alkenes act as nucleophiles

44
Q

Alkene reactions

A

Electrophillic addition, hydorgenation, hydration and hydrohalogenation

45
Q

What are alkynes

A

have a carbon to carbon triple bond

46
Q

What is Markovnikov’s rule

A

the route that makes the most stable carbocation is favoured and produces the major product

47
Q

What is syn addition

A

addition of two substituents to the same side of an unsaturated molecule

48
Q

What is anti addition

A

e addition of two substituents to opposite sides of an unsaturated molecule

49
Q

What are cycloalkanes

A

sp3 hybridised carbons and are therefore not planar. They have restricted rotation of C-C bonds in cyclic structures leading to conformational isomers

50
Q

What is a resonance structure

A

alternative single and double bonds

51
Q

Describe the structure of benzene

A

sp2 hybridised and is planar. Contains 6 electrons in pure p orbitals that are capable of overlapping. Electrons are delocalised around the ring and electrons both above and below are very stable

52
Q

Benzene reactions

A

electrophillic substitution. Delocalised electrons exposed above and below the plane of the molecule which is attractive to electrophiles (which must be very polarised)

53
Q

How can halogens become reactive enough to react with benzene

A

using Lewis acids e.g., AlX3

54
Q

What are activating side groups

A

electron donating so ring is more electron rich and substitution occurs at a faster rate e.g. OH. Take ortho or para positions

55
Q

What are deactivating side groups

A

electron withdrawing groups, ring becomes electron poor, substitution occurs at a slower rate e.g., COOH. Takes meta position

56
Q

Forces in carboxylic acids

A

hydrogen bonds on the OH but the rest of the molecule has london forces

57
Q

Properties of carboxylic acids

A

longer hydrocarbon, less soluble. Exist as dimers. High BP (due to H bonds)

58
Q

How can carboxylic acids act as an acid and a base

A

double bonded O can accept a proton (base). H from OH can be lost (acid)

59
Q

The effect of chain length on acidic properties of the carboxylic acid

A

longer the chain the weaker the acid (higher pKa), because alkyl groups push electron groups away causing an extra build up of negative charge on COO- making it less stable

60
Q

What is a carboxylate ion

A

has a negative charge which becomes delocalised between the 2 oxygen molecules

61
Q

Formation of an ester

A

carboxylic acid + alcohol. Catalysed by conc H2SO4/ HCl

62
Q

How to name an ester

A

yl (from alcohol). anoate (from carboxylic acid)

63
Q

Acid hydrolysis of an ester

A

alcohol + carboxylic acid

64
Q

Alkali hydrolysis of an ester

A

alcohol + carboxylate ion

65
Q

How are amides made

A

carboxylic acid + ammonia/amine via a condensation reaction

66
Q

What is a lactam

A

a cyclic amide. Constituent parts of some antibiotics like penicillin

67
Q

Electronegativity of halides

A

F, Cl and Br are more electronegative so the C- halogen bond is polar (unequal distribution of electrons)

68
Q

Why is F the most electronegative

A

most protons in the nucleus, and the valence electrons are the closest to the nucleus

69
Q

What is an optical isomer

A

have a chiral centre that creates non superimposable mirror images

70
Q

When is a carbon compound a chiral centre

A

if at least one carbon is bonded to 4 different atoms or groups

71
Q

What is achiral

A

doesn’t have 4 different atoms bonded to the carbon

72
Q

What are enantiomers

A

pairs of chiral molecule

73
Q

What is the +/- system for distinguishing between enantiomers

A

based on rotation for polarised light

74
Q

What is the R/S system for distinguishing between enantiomers

A

describes configuration of groups around a chiral

75
Q

What is the D/L system for distinguishing between enantiomers

A

D - hydroxy group on the right side. L - hydroxy group on the left side

76
Q

R and S system on distinguishing between enantiomers

A

Identify stereogenic (chiral) centre

Assign priority number to each group (higher atomic number is given higher priority. If 2 are the same asses the atoms that are attached to those atoms)

Arrange so lowest priority group is pointing away

Follow 1-2-3 around circle (if u look clockwise label ‘R’, anti-clockwise label ‘S’)

77
Q

What does rate of halogen reactions depend on

A

[nucleophile] and [carbon skeleton]

78
Q

Reactions of halogens

A

involved in both nucleophillic and electrophillic reactions

79
Q

If a stable halogen compound is formed what reaction mechanism was most likely used

A

SN1

80
Q

What influences carbocation stability

A

number of substituents and accessibility of carbon and nucleophile attack

81
Q

What are sigma bonds

A

end to end overlap of orbitals as atoms approach. Electrons of one atom are attracted to nucleus of the other. Continues until repulsion between the nuclei outweighs this attraction

82
Q

Bonding of carbon

A

has 2 unpaired electrons. Needs to be hybridisation of atomic orbitals. Forms 4 bonds

83
Q

Sp3 hybridisation

A

Methane has 4 bonds that are identical in length and have a bind angle of 109.5

Promoting a 2s electron into an empty 2p orbital gives 4 unpaired electrons. (2s1, 2p3)

But methane would have 4 bonds, 3 are the same and one would have a different length when they need to be the same

All 4 bonds in methane are equal length so atomic orbitals involved in the bind are equivalent

S and p orbitals are mixed to form hybrid orbitals

One s and 3 p orbitals are mixed so sp3 hybridisation

84
Q

sp2 hybridisation

A

Carbon only bonded to 3 atoms

Ethene: planar molecule with bond angle of 121.3 degrees

A 2s electron is promoted

So one s and 2 p orbitals hybridise together

These 3 hybrid orbitals can form one s bond each (one p orbital left over)

Bond angle of 121.3 degrees

The 2 pure p orbitals left over, overlap sideways to form a pi bond.

85
Q

sp hybridisation

A

E.g. ethyne

Hybridise one s and one p orbital to make 2 sp orbitals

2 pure p orbitals are ;eft over per carbon so they sideways overlap to form 2 pi bonds

Each carbon forms 2 sigma and 2 pi bonds

86
Q

What is homolytic cleavage

A

1 electron to each atoms, formation of radicals

87
Q

what is heterolytic cleavage

A

2 electrons transferred, formation of ion

Biological Chemistry (12 decks)

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