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Biochemistry > 2. Protein Structure and Function > Flashcards

2. Protein Structure and Function Flashcards

1
Q

What are the most abundant and functionally versatile macromolecules in living systems?

A

Proteins

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2
Q

What are amino acids?

A

Monomers that make up polypeptides

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3
Q

Which bonds are the alpha carbon of amino acids bonded to?

A
  • carboxylic acid group
  • amino group
  • R group (side chain)
  • hydrogen
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4
Q

T/F

All amino acids are chiral except glycine

A

True

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5
Q

We see the ___ isomers of amino acids in nature

A

L

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6
Q

Where is the carboxylic acids groups pKa typically at?

A

3

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7
Q

About what pKa do amino groups have?

A

9

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8
Q

T/F A zwitterion is overal neutral and has positive and negative groups

A

True

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9
Q

What is the 3 letter abbreviation for Glycine?

A

Gly

  • simplest amino acid
  • only amino acid that is not chiral
  • nonpolar
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10
Q

What is the 3 letter abbreviation for Alanine

A

Ala

nonpolar

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11
Q

What is the 3 letter abbreviation for Valine?

A

Val

  • forms a v in the structure
  • nonpolar
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12
Q

What is the 3 letter abbreviation for Leucine?

A

Leu

  • nonpolar
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13
Q

What is the 3 letter abbreviation for Isoleucine?

A

Ile

-nonpolar

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14
Q

What is the 3 letter abbreviation for Methionine?

A

Met

  • Nonpolar
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15
Q

What is the 3 letter abbreviation for Proline?

A

Pro

  • Nonpolar
  • 1st aromatic amino acid
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16
Q

What is the 3 letter abbreviation for Phenylalanine?

A

Phe

  • Nonpolar
  • Aromatic
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17
Q

What is the 3 letter abbreviation for Tryptophan?

A

Trp

  • nonpolar
  • 2 aromatic rings
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18
Q

What is the 3 letter abbreviation for Serine?

A

Ser

-polar uncharged

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19
Q

What is the 3 letter abbreviation for Threonine?

A

Thr

-polar uncharged

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20
Q

What is the 3 letter abbreviation for Tyrosine?

A

Tyr

  • aromatic
  • polar uncharged
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21
Q

What is the 3 letter abbreviation for Cysteine?

A

Cys

  • SH
  • polar uncharged
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22
Q

What is the 3 letter abbreviation for Asparagine?

A

Asn

-polar uncharged

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23
Q

What is the 3 letter abbreviation for Glutamine?

A

Gln

-polar uncharged

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24
Q

What is the 3 letter abbreviation for Lysine?

A

Lys

  • positively charged amino acids
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25
Q

What is the 3 letter abbreviation for Arginine?

A

Arg

  • positively charged amino acids
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26
Q

What is the 3 letter abbreviation for Histidine?

A

His

  • positively charged amino acids
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27
Q

What is the 3 letter abbreviation for Aspartate

A

Asp

  • negatively charged
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28
Q

What is the 3 letter abbreviation for Glutamate?

A

Glu

  • Negatively charged amino acids
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29
Q

Name the typical pKa of terminal a-carboxyl group

A

3.1

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30
Q

Name the typical pKa of aspartic acid and glutamic acid

A

4.1

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31
Q

Name the typical pKa of histidine

A

6.0

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32
Q

Name the typical pKa of terminal a-amino group

A

8.0

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33
Q

Name the typical pKa of cysteine

A

8.3

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34
Q

Name the typical pKa of tyrosine

A

10.9

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35
Q

Name the typical pKa of Lysine

A

10.8

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36
Q

Name the typical pKa of Arginine

A

12.5

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37
Q

Name the amino acid: Ala

A

Alanine

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38
Q

Name the amino acid: Arg

A

Arginine

39
Q

Name the amino acid: Asn

A

Asparagine

40
Q

Name the amino acid: Asp

A

Aspartic acid

41
Q

Name the amino acid: Cys

A

Cysteine

42
Q

Name the amino acid: Gln

A

Glutamine

43
Q

Name the amino acid: Glu

A

Glutamic acid

44
Q

Name the amino acid: Gly

A

Glycine

45
Q

Name the amino acid: His

A

Histidine

46
Q

Name the amino acid: Ile

A

Isoleucine

47
Q

Name the amino acid: Leu

A

Leucine

48
Q

Name the amino acid: Lys

A

Lysine

49
Q

Name the amino acid: met

A

Methionine

50
Q

Name the amino acid: Phe

A

Phenylalanine

51
Q

Name the amino acid:Pro

A

Proline

52
Q

Name the amino acid: Ser

A

Serine

53
Q

Name the amino acid: Thr

A

threonine

54
Q

Name the amino acid: Trp

A

Tryptophan

55
Q

Name the amino acid: Tyr

A

Tyrosine

56
Q

Name the amino acid: Val

A

Valine

57
Q

At pH = 2, what is the net charge on the amino acid leucine?

A

+1

58
Q

At pH = 1, what is the net charge on the amino acid aspartic acid?

A

+1

59
Q

At pH = 7, what is the net charge on the amino acid aspartic acid?

A

-1

60
Q

At pH = 11, what is the net charge on the amino acid aspartic acid (aspartate)?

A

-2

61
Q

What is the primary structure of amino acids?

A

The sequence of amino acids linked by peptide bonds

62
Q

Which bonds are present in primary amino acid structure?

A

peptide bonds

63
Q

What is the term for two amino acids linked together?

A

Dipeptide

64
Q

Is there rotation about the peptide bond?

A

No they are planar, no rotation around the bond

65
Q

What is the directionality of a polypeptide chain?

A

N-terminus to C-terminus

66
Q

T/F there are steric interactions that have to be taken into consideration in primary protein structure

A

True

67
Q

T/F

Polypeptides have directionality

A

True

68
Q

What is the net charge at pH = 5 on the tripeptide Tyr-His-Ala?

A

+1

69
Q

What is the net charge at pH = 12 on the tripeptide Cys-Val-Glu?

A

-3

70
Q

Almost all peptide bonds are _____ this prevents steric clashes between R groups

A

trans

71
Q

The bond between the alpha carbon and the amino group is the ____-

A

phi bond

72
Q

The bond between the alpha carbon and the carbonyl bond is the _____

A

psi bond

73
Q

What does a ramachandran plot show?

A

The favorable combination of phi and psi bonds. Dark green shows the most favorable

74
Q

How are protein structures determined?

A
  • x-ray crystallography
  • cryo-electron microscopy
  • AI –> alpha fold 2, a computer algorithm
75
Q

What is alpha fold 2?

A

A computer algorithm that can help determine protein structures

76
Q

What type of bonds/interactions contribute to the primary structure of a protein?

A

covalent bonds

77
Q

Define protein secondary structure:

A

Local folded protein structure that is due to interactions between atoms in the protein backbone (main chain)

78
Q

Who discovered the alpha helix?

A

Linus pauling

79
Q

What are the characteristics of alpha helices?

A
  • tightly coiled backbone
  • side chains extend outward
  • stabilized by hydrogen bonds between N-H group on one amino acid and C=O group (4 amino acid residues ahead)
  • 3.6 amino acid residues per turn
  • right handed helices in nature
80
Q

How many amino acid residues per turn in alpha helices?

A

3.6

81
Q

What are the characteristics of beta sheets?

A
  • links of beta strands running parallel or anti parallel
  • direction indicated by arrows in ribbon diagrams
  • most adopt a somewhat twisted shape
  • strands don’t need to be neighbors in amino acid sequence
82
Q

In the protein antiparallel beta sheet, which of the following is true?
A. The beta sheet is stabilized by hydrogen bonds between R groups
B. One strand can hydrogen bond to two other strands
C. One strand can hydrogen bond to one other strand
D. Hydrogen bonds are formed between and amino acid and the fourth amino acid ahead

A

One strand can hydrogen bond to two other strands

83
Q

What is the main type of bond/interaction that stabilizes protein structure?

A

Hydrogen bonds

84
Q

Define tertiary structure of proteins:

A

the overall 3d structure resulting from folding and covalent cross-linking of a polypeptide

85
Q

What are the characteristics of 3d protein structure?

A
  • result of the interaction between r groups
  • generally the interior consists almost entirely of nonpolar residues with polar residues on the outside
  • motifs
  • domains
86
Q

what are motifs?

A

combination of secondary structure with a particular role

  • **Super secondary structure
    ex. helix turn helix
87
Q

What are domains?

A

Compact globular units connected by a short polypeptide strand

ex. CD4 domains, same polypeptide but look like 4 globular units

88
Q

Cysteine residues each have a _____ group and these link to form _______ bonds

A

thiol
disulfide

This is how you get a perm, the solution put on the hair links covalent disulfide bonds

89
Q

Define quaternary structure:

A

multiple polypeptide chains (subunits) that assemble into a functional protein

  • subunits can be the same or different
  • nomenclature: alpha, beta, gamma
    Hemoglobin: alpha 2 beta 2 (tetramer)
90
Q

Define protein denaturation:

A

loss of secondary, tertiary, or quaternary structure of a protein

91
Q

What are the 3 ways proteins can be denatured?

A
  • heat
  • pH
  • kinetic energy
92
Q 
An enzyme is found to consists of two identical subunits. Which of the following would be an appropriate representation of the quaternary structure?
a2
ab
b2
ay
A

a2

93
Q

Disulfide bonds are formed between pairs of which amino acid?

A

Cysteine

Biochemistry (7 decks)

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