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My MCAT Study > Organic Chemistry- Nitrogen- and Phosphorus-Containing Compounds > Flashcards

Organic Chemistry- Nitrogen- and Phosphorus-Containing Compounds Flashcards

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MCAT flashcards
1
Q

What 3 elements make up 93% of the human body by weight?

A

Carbon
Hydrogen
Oxygen

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2
Q

What comprises 3.2% of body weight?

A

Nitrogen

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3
Q

What comprises 1% of human body weight?

A

Phosphorus

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4
Q

What are amino acids?

A

Dipolar molecules that come together through a condensation reaction, forming peptides.

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5
Q

What are considered proteins?

A

Larger, folded peptide chains

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6
Q

What is a better description of amino acids?

A

Containing an amino group and a carboxyl group attached to a single carbon atom (the alpha-carbon). The other two substituents of the alpha-carbon are a hydrogen atom and a side chain referred to as the R group.

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7
Q

The alpha-carbon is what in Amino acids?

A

A Chiral center

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8
Q

What is the simplist amino acid?

A

Glycine

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9
Q

Why is glycine an exception to the amino acids?

A

Because its R group is a hydrogen atom.

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10
Q

All naturally occuring amino acids in Eukaryotes (except glycine) are what?

A

Optically active, and all are L-isomers.

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11
Q

How is the Fischer projection of an amion accid drawn?

A

With the amino group on the left. L-amino acids have (S) configurations.

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12
Q

What amino acid is an exception to the (S) configuration? Why?

A

Cysteine which is (R) because of the change in priority caused by the sulfur in its R group

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13
Q

Amino acids are what type of molecules? Why?

A

Amphoteric molecules

Because of their acidic carboxyl group and basic amino group

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14
Q

What are amphoteric molecules?

A

They can act as both acids and bases.

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15
Q

How can amino acids act as both acids and bases?

A

They can take on a positive charge by being protonated, and carboxyl groups can take on a negative charge by being deprotonated.

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16
Q

When amino acid is put in solution, what does it do?

A

It will take on both of these charges, forming a dipolar ion or zwitterion.

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17
Q

How an amino acids act s depend on what? Example?

A

The pH of the environment.
In basic solutions, the amino acid can become fully deprotonated
In acidic solutions, it can become fully protonated.

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18
Q

Each amino acid has properties defined by what?

A

Its R group

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19
Q

The 20 Eukaryotic proteogenic amino acids can be grouped into what 5 categories?

A 
Nonpolar nonaromatic 
Aromatic
Polar
Negatively charged (acidic)
Positively charged (basic)
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20
Q

Nonpolar nonaromatic amino acids tend to have side chains that are what?

A

Saturated hydrocarbons
Cyclic with a secondary amine
Contains sulfur

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21
Q

What amino acids are nonpolar nonacromatic?

A 
Alanine
Valine
Leucine
Isoleucine
Methionine
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22
Q

Aromatic amino acids include what?

A

Tryptophan
Phenylalanine
Tyrosine

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23
Q

Nonpolar amino acids– both nonaromatic and aromatic– are what?

A

Also hydrophobic and tend to be sequestered in the interior of proteins

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24
Q

Polar amino acids tend to have what?

A

Terminal groups containing oxygen, nitrogen, or sulfur

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25
Q

What are polar amino acid examples?

A 
Serine
Theronine
Asparagine
Glutamine
Cysteine
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26
Q

What amino acids are included in negatively charged amino acids?

A

Aspartic acid and glutamic acid

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27
Q

What do negatively charged amino acids have?

A

Terminal carboxylate anions in their R groups

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28
Q

What amino acids are positively charged amino acids?

A

Arginine
Lysine
Histidine

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29
Q

What do positively charged amino acids have?

A

A protonated amino group in their R groups

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30
Q

What categories of amino acids are hydrophilic? What do they tend to form?

A

Polar
Acidic
and Basic amino acids
Tend to form hydrogen bond with water in aqueous solutions

31
Q

How are peptide bonds formed?

A

Amino acids undergo cocndensation reactions

32
Q

What are the molecules formed from peptide bonds called?

A

Polypeptides

33
Q

What are polypeptides?

A

Base unit of proteins

34
Q

What is the reverse reaction of peptide bonds? How is it catalyzed?

A

Hydrolysis

Catalyzed by strong acid or base

35
Q

Amides have how many resonance structures?

A

Two resonance structures

36
Q

What is the true structure of the amide bond?

A

A hybrid of partial double-bond character between the nitrogen atom and the carbonyl carbon

37
Q

The double-bond in amide bonds does what?

A

Limits rotation about the C-N bond, which adds to the rigidity and stability of the backbone of proteins.

38
Q

The single bonds in peptide bonds allow what?

A

Permit free rotation.

39
Q

What is step one of the stecker synthesis?

A

One starts with an aldehyde, ammonium chloride (NH4Cl) and potassium cyanide (KCN). The carbonyl oxygen is protonated, incresing the electrophilicity of the carbonyl carbon. Then, ammonia can attack the carbonyl carbon, forming an imine. The imine carbon is also susceptible to nucleophilic addition reactions; thus the CN- anion from KCN attacks, forming a nitrile group (-C=-N). Final molecule at the end of step 1 is an aminonitrile

40
Q

What is an aminonitrile?

A

A compound containing an amino group (-NH2) and a nitrile group.

41
Q

What happens in step 2 of strecker synthesis?

A

The nitrile nitrogen is protonated, increasing the electrophilicity of the nitril carbon. This is similar to protonating the oxygen of a carbonyl. A water molecule attacks, leading to the creation of a molecule with both imine and hydroxyl moieties on the same carbon. This imine is attacked by another equivalent of water. A carbonyl is formed, kicking off ammonia and creating the carboxylic acid functionality.

42
Q

Step 2 of the strecker synthesis is performed in what? And accelerated How?

A

Performed in aqueous acid and can be accelerated by the use of heat.

43
Q

What is the starting material for the strecker synthesis?

A

A planar carbonyl-containing compound.

44
Q

What is the product of strecker synthesis? Why?

A

A racemic mixture
The incoming nucleophiles are equally able to attack from either side of the carbonyl; thus both L- and D- amino acids can be generated through this process.

45
Q

How is the Gabriel (malonic-ester) Synthesis started?

A

Potassium phthalimide is reacted with diethyl bromomalonate.
With phthalimide as the nucleophile, the (secondary) substrate carbon as the electrophile, and bromine as the leaving group, this reaction generates a phthalimidomalonic ester.

46
Q

In the Gabriel synthesis phthalimide acts as what? Why?

A

Acidic and exists in solution as a nucleophilic anion.

47
Q

In the Gabriel synthesis, what does Diethylbromonalonate act as? Why?

A

Contains a secondary carbon bonded to bromine,

Acts as a good leaving group

48
Q

The Gabriel Synthesis set up should sound like what?

A

The Sn2 reaction

49
Q

What is the benefits of using a large nucleophile?

A

The bulkiness of this group creates steric hindrance, which prevents the substrate carbon from undergoing multiple substitions.

50
Q

In the Gabriel synthesis, instead of the substrate carbon undergoing multiple substitions what happens?

A

In the presence of base, this carbon (which is the alpha-carbon between two carbonyls) can easily be deprotonated. The molecule as a whole can then act as a nucleophile, attacking the substrate carbon of a bromoalkane.

51
Q

What happens in the second step of the Gabriel synthesis?

A

The molecule is hydrolyzed with strong base and heat. The phthalimide moiety is removed as phthalic acid (with two carboxylic acids). The malonic ester is hydrolyzed to a dicarboxylic acid with an amine on the alpha-carbon.

52
Q

What is the final step of the Gabriel synthesis?

A

The dicarboxylic acid, which is a 1,3-dicarbonyl, an be deccarboxylated through the addition of acid and heat. THe loss of a molecule of carbon dioxide results in the formation of the complete amino acid.

53
Q

What is the product of the gabriel synthesis? Why?

A

A racemic mixture because the Gabriel synthesis also starts with a racemi mixture.

54
Q

Why is phosphoric acid an important molecule biochemically?

A

The molecule forms the high-energy bonds that carry energy in adenosine triphosphate.

55
Q

In biochemical context, phosphoric acid is sometimes referred to as what?

A

A phosphate group or inorganic phosphate, denoted Pi

56
Q

At physiological pH, inorganic phosphate includes what molecule?

A

Molecules of both hydrogen phosphate (HPO4 2-) and dihydrogen phosphate (H2PO4-)

57
Q

Phosphorus is also found where? In what type of bonds?

A

The backbone of DNA in phosphodiester bonds

58
Q

What are phosodiesters?

A

Bonds linking the sugar moieties of the nucleotides.

59
Q

What is a pyrophosphate and how is it formed?

A

When a new nucleotide is joined to a growing strand of DNA by a DNA polymerase, it releases an ester dimer of phosphate

60
Q

What does the release of pyrophosphate provide?

A

The hydrolytic release of this molecule provides the energy for the formation of the new phosphodiester bond.

61
Q

When is pyrophosphate unstable? What happens?

A

Unstable in aqueous solution and is hydrolyzed to form two molecuesl fo inorganic phosphate, which can then be recycled to form high-energy bonds in ATP or for other purposes.

62
Q

What is referred to as organic phosphates? Why?

A

Nucleotides, such as ATP, GTP, and those in DNA.

Due to the presence of the phosphate group bonded to a carbon-containing molecule.

63
Q

How is phosphoric acid unique?

A

It has three acidic hydrogen, each with its own pKa.

64
Q

Phosphoric acid most properly refers to the form that predominates in What?

A

Strongly Acidic conditions, H3PO4

65
Q

In mildly acidic conditions, what hppens to phosphoric acid?

A

It loses a proton to become dyhydrogen phosphate, H2PO4

66
Q

In weakly basic solutions, what happnes to phosphoric acid?

A

It will readily lose a second proton to become hydrogen phosphate, HPO4

67
Q

What is the form of phosphoric acid that exists in strong basic solutions?

A

Phosphate PO4 3-

68
Q

What is the pKa for the loss of the first hydrogen in phosphoric acid?

A

2.15

69
Q

What is the pKa for the loss of the second hydrogen in phosphoric acid?

A

7.20

70
Q

What is the pKa for the loss of the third hydrogen in phosphoric acid?

A

12.32

71
Q

At a physiological pH of 7.4, what does it mean for dihydrogen phosphate and hydrogen phosphate?

A

They predominate in nearly equal proportions.

72
Q

What makes phosphates good buffers? Why?

A

The variety of pKa values

Because they can pick up or give off protons depending on the pH of the solution

73
Q

Adjacent phosphate groups on a nucleotide triphosphate experience what?

A

A large amount of repulsion because they are negatively charged.

74
Q

The energy released when a phosphate or pyrophosphate is cleaved is ___________? Why?

A

High. The adjacent phosphate groups combined with the ability of phosphate to stabilize up to three negatively charged.

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