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Organic Chemistry > Chapter 7 - Nitrogen Compounds > Flashcards

Chapter 7 - Nitrogen Compounds Flashcards

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1
Q

Define an amine

A

central nitrogen with 3 sigma bonds (to either hydrogen or carbon) and a lone pair

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2
Q

Imine structure

A
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3
Q

Secondary amine structure

A
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4
Q

Hydroxylamine structure

A
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5
Q

Hydrazine structure

A
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6
Q

Oxime structure

A
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7
Q

What is the base strength (pKb) of amines?

A

They are weak bases.

pKb between 3 and 5

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8
Q

Which amine substitution is most basic? Why?

A

secondary amine: alkyl group substitution affects sterics (makes it more hindered), but is balanced by the inductive effect (donates greater electron density)

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9
Q

Equation: equilibrium constant for proton-transfer reactions

A

Keq = 10pKa(product acid) - pKa(reactant acid)

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10
Q

Equation: Henderson-Hasselbalch pH

A

pH = pKa(protonated species) + log [deprotonated species]/[protonated species]

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11
Q

Do alkoxy groups donate or withdraw electron density by resonance?

A

They donate electron density.

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12
Q

What is the product of ammonia reacted with an alkyl halide?

A

tertiary amine (maybe quaternary)

Amines tend to undergo multiple additions with alkyl halides.

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13
Q

What is formed when an amine reacts with an ester?

A

amide

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14
Q

What is formed when an amine reacts with a carboxylic acid?

A

amide

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15
Q

How does aromaticity affect basicity?

A

Since electron density is tied up in the aromatic ring, it is less available for donation, reducing the compounds basicity.

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16
Q

What is formed when an amide is reacted with LiAlH4?

A

It is reduced to an amine.

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17
Q

What is formed when an imine is reacted with NaBH4?

A

It is reduced to an amine.

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18
Q

For reactions of amines, what are two general results?

A

Either:

  • leaving group is displaced
  • water is formed as a side procuct
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19
Q

What happens in a Hofmann elimination reaction?

A

A primary amine is reacted with excess methyl iodide, forming a quaternary amine cation. When reacted with Ag2O and heat, it undergoes E2 elimination, kicking the tertiary amine off, and forming a less substituted alkene.

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20
Q

Is an aldehyde or ketone more electrophilic?

A

aldehyde is more electrophilic

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21
Q

What is formed when a primary amine is reacted with an aldehyde/ketone?

A

imine + water

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22
Q

With what compounds does an amine tautomerize?

A

enamine

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23
Q

What is formed when a secondary amine is reacted with an aldehyde/ketone?

A

enamine

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24
Q

As amides become increasingly substituted, how does this affect the compound’s boiling point?

A

Boiling point is lowered with increasing substitution, because the hydrogens on an amide nitrogen can hydrogen bond with the oxygen on the carbonyl.

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25
Q

What is formed in a Hofmann Rearrangment?

A

A primary amide rearranges to form a primary amine and carbon dioxide.

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26
Q

Naturally occuring amino acids have what stereochemistry at carbon 2? What is an exception?

A

S-stereochemistry (except cysteine has R). All of these are L.

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27
Q

What is the pKa of the side chain in lysine?

A

10.8

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28
Q

What is the pKa of the side chain in aspartic acid?

A

3.9

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29
Q

What is the pKa of the side chain in glutamic acid?

A

4.2

30
Q

What is the pKa of the side chain in arginine?

A

13.2

31
Q

What is the pKa of the side chain in histidine?

A

6

32
Q

Is the formation of a polypeptide disulfide bridge oxidation or reduction? Which amino acid offers this function?

A

cysteine: oxidation

33
Q

Which amino acid causes structural turns in a polypeptide?

A

proline because it can’t rotate freely about its sigma bonds

34
Q

What is meant by the ioselectric pH?

A

the pH at which a zwitterion exists in highest concentration (neutral)

35
Q

Does the zwitterion form of an amino acid have a high or low melting point and why?

A

It is high because it has opposite charges, making it a salt.

36
Q

How can the isoelectric point be calculated for different amino acids?

A

For most amino acids, it is the first equivalence point (pI = (pKa1 + pKa2)/2)

For Lysine, Arginine, and Histidine, it is the second equivalence point (pI = (pKa2 + pKa3)/2)

37
Q

If a protein has a charge of +6 when it is fully protonated, between what pKa’s will its isoelectric point exist?

A

between pKa 6 and 7

38
Q

What is the rule for finding the isoelectric point based on the number of basic amino acids in a protein?

A

Sum the number of basic amino acids +1, and pI will be between the pKa with that value subscript and one sequentially higher.

39
Q

In a polypeptide, which site will deprotonate at pKa1?

A

the carboxyl terminal

40
Q

Equation: isoelectric point

A

pI = (pka1 + pka2)/2

41
Q

What is the pKa of the side chain in cysteine?

A

8.3

42
Q

What is the pKa of the side chain in serine?

A

13

43
Q

What is the pKa of the side chain in tyrosine?

A

10.1

44
Q

As a general rule, acidic amino acids have pI values less than what?

A

less than 5.5

45
Q

As a general rule, basic amino acids have pI values greater than what?

A

greater than 7.5

46
Q

As a general rule, non-acidic/basic amino acids have a pI value in what range?

A

5.5-7.5

47
Q

What is primary structure in a protein?

A

the sequence of amino acids within the protein

48
Q

What is secondary structure in a protein?

A

localized folding of the amino acids into their natural configuration within the protein (α-helix and β-pleated sheets)

49
Q

What is the driving force behind protein secondary structure?

A

hydrogen bonding

50
Q

How does the oxidation of an un-crosslinked protein compare with that of a crosslinked protein?

A

The crosslinked protein is more oxidized.

51
Q

What is the driving force behind tertiary structure of a protein?

A

disulfide bonds

52
Q

How can disulfide bonds be broken within a protein? What is a typical reagent that does this?

A

They can be reduced, thus denaturing a protein (typically use β-mercaptoethanol)

53
Q

Does enthalpy or entropy favor cross-linking in a protein?

A

enthalpy

54
Q

What is tertiary structure in a protein?

A

the overall folding of a protein (typically globular)

55
Q

What is the lowest level of protein structure changes between lipid and aqeuous environments?

A

secondary structure

56
Q

In gel electrophoresis, which ions migrate to the cathode and which to the anode?

A

Cations migrate to the cathode, while anions migrate to the anode.

57
Q

Equation: forces on particles in electrophoresis

A

ma = qE - Fresistive drag

58
Q

What are the two types of gel electrophoresis used to separate protein fragments?

A
  • Isoelectric focusing: pI differences
  • SDS-PAGE: mass differences
59
Q

Describe isoelectric focusing gel electrophoresis

A

The gel contains a pH gradient and the charged species migrate through the gel until they reach a pH equal to their pI.

60
Q

Describe SDS-PAGE gel electrophoresis

A

SDS (sodium dodecyl sulfate) is added to the protein mixture, making every protein fragment negatively charged. More massive fragments can take on a greater magnitude of charge. All fragments have the same mass-to-charge ratio, so they separate only based on size difference, because they experience the same electric field. Small fragments migrate faster because they experience less drag resistance through the gel.

61
Q

An amino acid in an environment with a pH greater than its pI will be of what charge?

A

negative

62
Q

An amino acid in an environment with a pH less than its pI will be of what charge?

A

positive

63
Q

Describe affinity (ion-exchange) chromatography for proteins

A

It separates by the affinity of charged proteins for oppositely charged sites on the polymer in the column (stationary phase). Based on the solution pH, certain proteins will be negatively or positively charged. Proteins carrying the same charge as the column will elute.

64
Q

Describe size-exclusion (gel-filtration) chromatography

A

A column is filled with agarose beads or dextran which has natural pores of varying size. As the solution flows down the column, smaller species get caught in the pores, while larger proteins do not and elute in less time. (Doubling elution time typically corresponds to half the molecular mass)

65
Q

What is the first step in sequencing a protein?

A

Treat with urea to break hydrogen bonds and β-mercopthoethanol to break disulfide bonds.

66
Q

After tagging, how can fragments be identified in protein sequencing?

A

Enzymes can be used that specifically cleave certain residues at either their N- or C-terminus.

67
Q

What is Edman’s reagent used for? What is its structure?

A

It sequentially removes each amino acid from a protein starting from the amino terminal.

phenylisothiocyanate

68
Q

What happens when a protein undergoes hydrolysis?

A

All of its amide peptide bonds are cleaved.

69
Q

What is unique about the amino acids in bacterial cell walls?

A

There is a cross-link between D-alanine (naturally occuring!) and glycine.

70
Q

What is the nucleophilicity of amines?

A

They are good nucleophiles and frequently undergo SN2 reactions.

71
Q

In protein sequencing, how can the first amino acid be identified?

A

It must be tagged with Sanger’s reagent (2,4-dinitrofluoribenzene) which binds to the amino terminal of the protein. Complete acid hydrolysis of the protein (6M HCl) will then yield all of the component amino acids.

Organic Chemistry (6 decks)

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