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CHEM 1570: Intro to Organic and Biological Chemistry > Final Exam > Flashcards

Final Exam Flashcards

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1
Q

Draw the carboxylic acid functional group.

A

Carbonyl w/ an -OH group

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2
Q

Draw the acid chloride functional group.

A

Carbonyl w/ an -Cl group

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3
Q

Draw the acid anhydride functional group.

A

Carbonyl w/ an -another carbonyl group bonded by and -O- between them

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4
Q

Draw the ester functional group.

A

Carbonyl w/ an -OR’ group

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5
Q

Draw the amide functional group.

A

Carbonyl w/ an -NH2 or -NR2 group

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6
Q

Draw the thioester functional group.

A

Carbonyl w/ an -SR’ group

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7
Q

Draw the acyl phosphate functional group.

A

Carbonyl w/ a phosphate group

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8
Q

Draw the mechanism for a standard nucleophilic acyl substitution reaction. Use Butanoic Acid + Methanol —> Butanoate as the reference reaction.

A

First step: Protonation
Tetrahedral Intermediate
Last Step: Deprotonation

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9
Q

What is a nucleophile?

A

Atoms or functional groups w/ lone pairs of e- that can be used to make bonds

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10
Q

What is an electrophile?

A

Atoms or functional groups form bonds w/ nucleophiles by accepting their free lone pair of e- to make bonds.

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11
Q

What are the three features of nucleophile addition to carbonyls?

A
  • Proton (H+) transfer
  • Nucleophile addition to the electrophile/ Nucleophilic
    attack
  • e- come down from O- and kicks off a good leaving
    group.
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12
Q

Why can’t you do a nucleophilic substitution w/ aldehyde or ketone?

A

Aldehyde and Ketones do not provide any viable leaving groups needed to do a substitution reaction. If you add the nucleophile to the aldehyde and ketone, you’ll make a hemiacetal and hemiketal but they will still maintain the original substituents.

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13
Q

What makes a good leaving group?

A

Good leaving groups are weak bases.

  • If the conjugate acids are strong then the base is weak,
    thus making it a good leaving group.
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14
Q

What determines base strength?

A
  • Conjugate bases of weak acids are good bases
  • Nitrogen w/ free lone pairs of e- are good bases
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15
Q

What are the 8 carbonyl functional groups we discussed in class?

A
  • Carboxylic Acid
  • Acid Chloride
  • Acid Anhydride
  • Ester
  • Amide
  • Thioester
  • Acyl Phosphate
  • Carboxylate
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16
Q

Rank the 7 carbonyl functional groups we discussed in class in order of leaving group strength

A

Best Leaving Group: Acid Chloride, Acyl Phosphate
Acid Anhydride, Thioester
Ester, Carboxylic Acid
Amide
Worst Leaving Group: Carboxylate

17
Q

Draw the carboxylate functional group

A

Carbonyl w/ a -O- group

18
Q

What do you do when you have a carboxylate ion available to react with in a nucleophilic substitution reaction?

A

Create a acyl phosphate reaction intermediate

19
Q

What does creating an acyl phosphate reaction intermediate do?

A

Because acyl phosphate is the most reactive carboxylic acid derivative (next to acid chloride), when you use it as a reaction intermediate, you can go “downhill” in reactive carboxylic aid derivatives for reactions.

20
Q

How does the process of going from a carboxylate ion to an acyl phosphate work?

A

By coupling the energetically UNFAVORABLE reaction of going from a carboxylate ion to an acyl phosphate with the energetically FAVORABLE reaction of converting ATP to ADP (or AMP).

21
Q

What is coupling?

A

Coupling involves doing an energetically unfavorable reaction simultaneously with an energetically favorable reaction to balance the reaction out.

22
Q

What is the result of “mixing” (reacting) a carboxylic acid w/ an amine (NH3)?

A

The result of the reaction will result in an acid-base reaction, NOT a nucleophilic substitution reaction.

23
Q

Why does mixing carboxylic acid w/ amines result in acid-base reactions?

A

The amine (NH3) will act as a base taking the H+ from the carboxylic acid. The result will be the extremely unreactive carboxylate ion and an NH4(+), which is no longer a nucleophile. Since NH4(+) has no free lone pairs of e- for bonding, other reactions cannot occur.

24
Q

What is physiological pH?

A

7-ish

25
Q

Draw what an amino acid looks like a physiological pH

A

On the LEFT side of the R group is NH4(+)

On the RIGHT side of the R group is the carboxylate ion

26
Q

What is the name of an amino acid at physiological pH?

Hint: What is the name of a molecule that has a positive
and negative net charge that adds to 0.

A

Zwitterion

27
Q

Is the NH4(+) group of an amino acid predominately protonated or deprotonated at physiological pH?

A

Predominantly protonated

28
Q

Is the carboxylate ion predominantly protonated or deprotonated at physiological pH?

A

Predominately deprotonated

29
Q

Proteins

A

Proteins are long chains of amino acids connected by peptide bonds

30
Q

What are peptide bonds?

A

Peptide bonds are repeating bonds of amino acids

31
Q

What is the side of the NH3 group of an amino acid called?

A

The N-terminus

32
Q

What is the side of the carboxylate ion group of an amino acid called?

A

The C-terminus

33
Q

Which direction are amino acids added to proteins?

A

From the N-terminus —–> C-terminus

34
Q

Why don’t amino acids want to bond together?

A

Because the N-terminus end of an amino acid and the C-terminus end of an amino acid do not mix.

Remember, they do not result in nucleophilic substitution reactions. Rather, they result in acid-base reactions.

35
Q

How do you overcome the problem of amino acids not wanting to bond together?

A

By creating an acyl-phosphate intermediate through the process of phosphorylation.

Once you phosphorylate the amino acid and replace the carboxylate ion w/ an acyl phosphate, you can go “downhill” in reactive carboxylic acid derivatives to get to an amide (in this case it would be an NH3).

36
Q

Draw the mechanism of joining amino acids

A
  1. Phosphorylate the carboxylate to form AMP (releases
    PiPi) and create an acyl-phosphate intermediate
  2. Add a aa1-ester-tRNA (amino acid 1-ester) to from the
    tetrahedral intermediate
  3. Bring down the e- on O- to kick off the acyl
    phosphate. At the same time the bond connecting the
    phosphate and the rest of the molecule will
    deprotonate the aa1-ester-tRNA.
  4. Deprotonate NH3(+) on aa2-ester-tRNA to make it
    nucleophilic
  5. Add aa2-ester-tRNA to aa1-ester-tRNA by making a
    tetrahedral intermediate
  6. Bring down e- on O(-) to kick off O-tRNA1. The bond
    holding O-tRNA1 and the rest of the molecule will
    deprotonate NH2(+) to make the amide join the
    two amino acids.
  7. (After doing those last steps over and over, the stop
    codon will come and this will happen) Release the nth
    tRNA from the protein and make the carboxylate ion
    using water (creates one more tetrahedral
    intermediate).

CHEM 1570: Intro to Organic and Biological Chemistry (4 decks)

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