Chapter 1. Amino Acids, Peptides, and Proteins Flashcards Preview

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

Flashcards in Chapter 1. Amino Acids, Peptides, and Proteins Deck (93):
1

What are the four properties of proteinogenic amino acids?

  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. 

2

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

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

3

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

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

4

Which amino acids are nonpolar, nonaromatic?

  • Glycine
  • Alanine
  • Valine
  • Leucine
  • Isoleucine
  • Methionine
  • Proline

5

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

Its R-group is a hydrogen atom. 

 

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

6

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

Methionine and Cysteine

7

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

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

8

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

Proline

9

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

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

10

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

pro, p

11

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

ala, a

12

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

val, v

13

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

leu, l

14

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

ile, i

15

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

met, m

16

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

gly, g

17

What is the name of the following amino acid?

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Glycine

18

What is the name of the following amino acid?

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Alanine

19

What is the name of the following amino acid?

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Valine

20

What is the name of the following amino acid?

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Leucine

21

What is the name of the following amino acid?

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Isoleucine

22

What is the name of the following amino acid?

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Methionine

23

What is the name of the following amino acid?

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Proline

24

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

  • Tryptophan (nonpolar)
  • Phenylalanine (nonpolar)
  • Tyrosine (polar)

25

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

trp, w

26

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

phe, f

27

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

tyr, y

28

What is the name of the following amino acid?

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Tryptophan

29

What is the name of the following amino acid?

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Phenylalanine

30

What is the name of the following amino acid?

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Tyrosine

31

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?

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

32

Which amino acids are considered to be polar?

  • Serine
  • Threonine
  • Asparagine
  • Glutamine
  • Cysteine

33

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

ser, s

34

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

thr, t

35

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

asn, n

36

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

gln, q

37

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

cys, c

38

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

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

39

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

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

40

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

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

41

What is the name of the following amino acid?

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Serine

42

What is the name of the following amino acid?

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Threonine

43

What is the name of the following amino acid?

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Asparagine

44

What is the name of the following amino acid?

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Glutamine

45

What is the name of the following amino acid?

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Cysteine

46

Why are serine and threonine considered to be polar?

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

47

Which amino acids are considered to be basic?

  • Arginine 
  • Lysine
  • Histidine

48

Which amino acids are considered to be acidic?

  • Aspartic Acid
  • Glutamic Acid

49

Fill in the blanks. 

 

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

 

 

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

50

What is the name of the following amino acid?

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Aspartic Acid

51

What is the name of the following amino acid?

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Glutamic Acid

52

What is the name of the following amino acid?

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Arginine

53

What is the name of the following amino acid?

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Lysine

54

What is the name of the following amino acid?

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Histidine

55

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

arg, r

56

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

lys, k

57

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

his, h

58

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

asp, d

59

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

glu, e

60

Which amino acid has three nitrogens in its side chain?

Arginine

 

61

Which amino acid has an imidazole ring? Explain.

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

62

Which amino acids are considered to be hydrophobic?

  • Alanine
  • Leucine
  • Isoleucine
  • Valine
  • Phenylalanine

63

Which amino acids are considered to be hydrophilic?

  • Histidine
  • Arginine
  • Lysine
  • Glutamate
  • Glutamine
  • Aspartate
  • Asparagine

64

What is the difference between hydrophobic and hydrophilic?

  • 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

Amino acids are said to be amphoteric species. Why?

  • 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

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

Protonated. 

 

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

67

Fill in the blank. 

 

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

Deprotonated. 

 

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

68

What is the pKa of a molecule?

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

69

Fill in the blanks. 

 

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

~2; ~9-10

70

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

The pH at which the molecule is electrically neutral. 

71

Fill in the blank. 

 

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

buffer

72

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

less than 6; greater than 6

73

What are peptides composed of?

Amino acid subunits, which are also called residues. 

74

Fill in the blanks. 

 

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

Oligopeptides; polypeptides

75

Fill in the blank. 

 

The residues in peptides are joined together by ____. 

peptide bonds

76

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

  • 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

How are peptide bonds formed?

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

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78

Fill in the blanks. 

 

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

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

79

Fill in the blanks. 

 

Peptide bonds are broken by ____ because ____. 

hydrolysis; it requires water

80

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?

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

81

Which protein structure is a linear arrangement of amino acids?

Primart

82

Which protein structure encodes all the information needed for coding?

Primary

83

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

Primary

84

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

Secondary

85

What are the two common secondary structures of a protein?

alpha-helices and beta-pleated sheets

86

How are α-helices stabilized?

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

87

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

Tertiary

88

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

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

89

What are disulfide bonds?

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

90

What are molten globules?

Intermediate states in the folding of a protein. 

91

Finish the sentence. 

 

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

more than one polypeptide chain. 

92

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

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

93

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

High heat or solutes (breaking disulfide bonds)