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MCAT Biochemistry > Chapter 1. Amino Acids, Peptides, and Proteins > Flashcards

Chapter 1. Amino Acids, Peptides, and Proteins Flashcards

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MCAT flashcards
1
Q

What are the four properties of proteinogenic amino acids?

A
  1. There is a central carbon with an amino group, carboxyl group, side chain, and hydrogen atom.
  2. All are α-amino acids.
  3. All are chiral (except for glycine).
  4. All are L-isomers.
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2
Q

Is the following an L-amino acid or D-amino acid? Explain.

A

L-amino acid. The amino group is on the left side.

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3
Q

Is the following an L-amino acid or D-amino acid? Explain.

A

D-amino acid. The amino group is on the right side.

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4
Q

Which amino acids are nonpolar, nonaromatic?

A
  • Glycine
  • Alanine
  • Valine
  • Leucine
  • Isoleucine
  • Methionine
  • Proline
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5
Q

Glycine is the only proteinogenic amino acid that is considered achiral. Why?

A

Its R-group is a hydrogen atom.

*Remember: A molecule is chiral if it has four different groups attached to it.

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6
Q

Which two amino acids contain a sulfur atom in their side chain?

A

Methionine and Cysteine

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7
Q

Methionine and cysteine both contain sulfur in their side chain. Why is methionine considered to be nonpolar, while cysteine is considered to be polar?

A

The sulfur in methionine has a methyl group attached to it, which makes it nonpolar.

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8
Q

Which amino acid has the amino group attached to the α-carbon?

A

Proline

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9
Q

The amino group in proline is only attached to the α-carbon, which creates a ring. What effects does the ring in proline have?

A

The ring causes flexibility constraints, which limits proline’s position on a protein and effects its role in secondary structures.

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10
Q

What are the 3-letter and 1-letter abbreviations for proline?

A

pro, p

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11
Q

What are the 3-letter and 1-letter abbreviations for alanine?

A

ala, a

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12
Q

What are the 3-letter and 1-letter abbreviations for valine?

A

val, v

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13
Q

What are the 3-letter and 1-letter abbreviations for leucine?

A

leu, l

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14
Q

What are the 3-letter and 1-letter abbreviations for isoleucine?

A

ile, i

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15
Q

What are the 3-letter and 1-letter abbreviations for methionine?

A

met, m

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16
Q

What are the 3-letter and 1-letter abbreviations for glycine?

A

gly, g

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17
Q

What is the name of the following amino acid?

A

Glycine

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18
Q

What is the name of the following amino acid?

A

Alanine

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19
Q

What is the name of the following amino acid?

A

Valine

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20
Q

What is the name of the following amino acid?

A

Leucine

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21
Q

What is the name of the following amino acid?

A

Isoleucine

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22
Q

What is the name of the following amino acid?

A

Methionine

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23
Q

What is the name of the following amino acid?

A

Proline

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24
Q

Which amino acids are considered to be aromatic? State whether each one is polar or nonpolar.

A
  • Tryptophan (nonpolar)
  • Phenylalanine (nonpolar)
  • Tyrosine (polar)
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25
Q

What are the 3-letter and 1-letter abbreviations for tryptophan?

A

trp, w

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26
Q

What are the 3-letter and 1-letter abbreviations for phenylalanine?

A

phe, f

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27
Q

What are the 3-letter and 1-letter abbreviations for tyrosine?

A

tyr, y

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28
Q

What is the name of the following amino acid?

A

Tryptophan

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29
Q

What is the name of the following amino acid?

A

Phenylalanine

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30
Q

What is the name of the following amino acid?

A

Tyrosine

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31
Q

Phenylalanine and tyrosine both have a benzyl group in their side chain. Why is phenylalanine considered to be nonpolar, while tyrosine is considered to be polar?

A

Tyrosine has a hydroxyl group attached to its benzyl group, while phenylalanine does not.

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32
Q

Which amino acids are considered to be polar?

A
  • Serine
  • Threonine
  • Asparagine
  • Glutamine
  • Cysteine
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33
Q

What are the 3-letter and 1-letter abbreviations for serine?

A

ser, s

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34
Q

What are the 3-letter and 1-letter abbreviations for threonine?

A

thr, t

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35
Q

What are the 3-letter and 1-letter abbreviations for asparagine?

A

asn, n

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36
Q

What are the 3-letter and 1-letter abbreviations for glutamine?

A

gln, q

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37
Q

What are the 3-letter and 1-letter abbreviations for cysteine?

A

cys, c

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38
Q

Asparagine and glutamine have a nitrogen in their side chain. What is a characteristic of the nitrogen atom?

A

The nitrogen in their side chain does not gain or lose protons with changes in pH.

39
Q

Proteinogenic amino acids are considered to be L-isomers. This translates to (S)-absolute configuration. Which amino acid has an (R)-absolute configuration? Explain.

A

Cysteine. The -CH2SH bond has priority over the -COOH bond.

40
Q

Cysteine’s side chain is said to be prone to oxidation. Why?

A

The -SH bond is weaker than the -OH bond.

41
Q

What is the name of the following amino acid?

A

Serine

42
Q

What is the name of the following amino acid?

A

Threonine

43
Q

What is the name of the following amino acid?

A

Asparagine

44
Q

What is the name of the following amino acid?

A

Glutamine

45
Q

What is the name of the following amino acid?

A

Cysteine

46
Q

Why are serine and threonine considered to be polar?

A

They have an -OH group in their side chain that makes them polar and capable of hydrogen bonding.

47
Q

Which amino acids are considered to be basic?

A
  • Arginine
  • Lysine
  • Histidine
48
Q

Which amino acids are considered to be acidic?

A
  • Aspartic Acid
  • Glutamic Acid
49
Q

Fill in the blanks.

____ amino acids have a positive charge, while ____ amino acids have a negative charge.

A

Basic amino acids have a positive charge, while acidic amino acids have a negative charge.

50
Q

What is the name of the following amino acid?

A

Aspartic Acid

51
Q

What is the name of the following amino acid?

A

Glutamic Acid

52
Q

What is the name of the following amino acid?

A

Arginine

53
Q

What is the name of the following amino acid?

A

Lysine

54
Q

What is the name of the following amino acid?

A

Histidine

55
Q

What are the 3-letter and 1-letter abbreviations for arginine?

A

arg, r

56
Q

What are the 3-letter and 1-letter abbreviations for lysine?

A

lys, k

57
Q

What are the 3-letter and 1-letter abbreviations for histidine?

A

his, h

58
Q

What are the 3-letter and 1-letter abbreviations for aspartic acid?

A

asp, d

59
Q

What are the 3-letter and 1-letter abbreviations for glutamic acid?

A

glu, e

60
Q

Which amino acid has three nitrogens in its side chain?

A

Arginine

61
Q

Which amino acid has an imidazole ring? Explain.

A

Histidine. An imidazole ring is an aromatic ring with two nitrogen atoms.

62
Q

Which amino acids are considered to be hydrophobic?

A
  • Alanine
  • Leucine
  • Isoleucine
  • Valine
  • Phenylalanine
63
Q

Which amino acids are considered to be hydrophilic?

A
  • Histidine
  • Arginine
  • Lysine
  • Glutamate
  • Glutamine
  • Aspartate
  • Asparagine
64
Q

What is the difference between hydrophobic and hydrophilic?

A
  • Hydrophobic
    • Water-hating.
    • Amino acids with long alkyl side chains.
    • More likely to be found in the interior of proteins, away from water.
  • Hydrophobic
    • Water-loving.
    • Amino acids that are charged.
    • More likely to be found on the surface of proteins.
65
Q

Amino acids are said to be amphoteric species. Why?

A
  • They have an acidic carboxylic acid and basic amino group.
  • They can either accept a proton or donate a proton.
  • How they react depends on their pH.
66
Q

If the pH of an amino acid is less than the pKa, then it is ____.

A

Protonated.

*Remember: Protonated means that it gains electrons. In this state, the amino has an NH3+ and COOH group.

67
Q

Fill in the blank.

If the pH of an amino acid is greater than the pKa, then it is said to be ____.

A

Deprotonated.

*Remember: Deprotonated means that it loses electrons. In this state, the amino has an NH2 and COO- group.

68
Q

What is the pKa of a molecule?

A

The pH at which half of the molecules of that species are deprotonated.

69
Q

Fill in the blanks.

The pKa of COOH is ____, while the pKa of NH2 is ____.

A

~2; ~9-10

70
Q

What is the isoelectric point (pI) of a molecule?

A

The pH at which the molecule is electrically neutral.

71
Q

Fill in the blank.

When the pH of a solution is equal to the pKa, the solution acts as a ____.

A

buffer

72
Q

The pI of acidic amino acids is ____, while the pI of basic amino acids is ____.

A

less than 6; greater than 6

73
Q

What are peptides composed of?

A

Amino acid subunits, which are also called residues.

74
Q

Fill in the blanks.

____ are peptides that contain 2-20 amino acid residues, while ____ are peptides that contain more than 20 amino acid residues.

A

Oligopeptides; polypeptides

75
Q

Fill in the blank.

The residues in peptides are joined together by ____.

A

peptide bonds

76
Q

The residues in peptides are joined together by peptide bonds. What are three characteristics of this bond?

A
  • It is a specialized form of an amide bond.
  • The C-N bond has a partial double bond character.
  • Rotation around this bond is limited.
77
Q

How are peptide bonds formed?

A

It forms between the -COO- group of one amino acid and the NH3+ group of another amino acid.

78
Q

Fill in the blanks.

The formation of a peptide bond is an example of a ____ reaction because ____.

A

condensation/dehydration; it results from the removal of a water molecule

79
Q

Fill in the blanks.

Peptide bonds are broken by ____ because ____.

A

hydrolysis; it requires water

80
Q

Peptide bonds are broken by hydrolysis since water is required. Who hydrolytic enzymes used in hydrolysis are trypsin and chymotrypsin. What is the difference between these two enzymes?

A
  • Trypsin cleaves at the carboxyl end of arginine and lysine.
  • Chymotrypsin cleaves at the carboxyl end of phenylalanine, tryptophan, and tyrosine.
81
Q

Which protein structure is a linear arrangement of amino acids?

A

Primart

82
Q

Which protein structure encodes all the information needed for coding?

A

Primary

83
Q

Which protein structure is stabilized by the formation of covalent peptide bonds between adjacent amino acids?

A

Primary

84
Q

Which protein structure is primarily the result of hydrogen bonding between nearby amino acids?

A

Secondary

85
Q

What are the two common secondary structures of a protein?

A

alpha-helices and beta-pleated sheets

86
Q

How are α-helices stabilized?

A

By intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom four residues down the chain.

87
Q

Which protein structure is the protein’s three-dimensional shape?

A

Tertiary

88
Q

What are two ways that the tertiary structure of a protein can be determined?

A
  • Hydrophobic and hydrophilic interactions between (R) groups.
  • Creating salt bridges (disulfide bonds).
89
Q

What are disulfide bonds?

A

Bonds that form when two cysteine molecules become oxidized to form cystine.

90
Q

What are molten globules?

A

Intermediate states in the folding of a protein.

91
Q

Finish the sentence.

The quaternary structure of a protein only exists for proteins that contain ____.

A

more than one polypeptide chain.

92
Q

The quaternary structure of a protein is said to induce cooperativity/allosteric effects. What does this mean?

A

One subunit can undergo conformational or structural changes, which can either enhance or reduce the activity of the other subunits.

93
Q

What are the two common ways that a protein can be denatured?

A

High heat or solutes (breaking disulfide bonds)

MCAT Biochemistry (3 decks)

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