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XX. BioChemistry > Chp 4: Protein Structure > Flashcards

Chp 4: Protein Structure Flashcards

1
Q

What are polymers made of proteins called?

A

Amino Acids

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2
Q

Draw the general structure of an amino acid at physiological pH

A
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3
Q

Under what conditions can cysteine form a disulfide bond?

A

Oxidative conditions

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4
Q

What is the approximate pKa of ionizable Asp?

A

4.0

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5
Q

What is the approximate pKa of ionizable His?

A

6.0

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6
Q

What is the approximate pKa of ionizable Glu?

A

4.0

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7
Q

What is the approximate pKa of ionizable NH3+ N-terminus?

A

9.0

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8
Q

What is the approximate pKa of ionizable Cys?

A

8.0

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9
Q

What is the approximate pKa of ionizable Tyr?

A

10.5

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10
Q

What is the approximate pKa of ionizable Lys?

A

10.5

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11
Q

What is the approximate pKa of ionizable Arg?

A

12.5

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12
Q

Relative abundance of amino acids in proteins

A

In nature, Leucine is the most abundant and Tryptophan is the least abundant

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13
Q

Average MW of an amino acid

A

110 Da when found in a protein

1 Da (Dalton) = 1 atomic mass unit (amu)

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14
Q

How the peptide bond is formed

A

Peptide bonds are made by condensation reactions. Amino acids in the peptide are called “amino acid residues” because only the residue atoms remain

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15
Q

Meaning of polypeptide chain-related terms: amino acid residue, amino- and carboxyl-terminal residues, and chain directionality

A
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16
Q

Properties of the peptide bond

A

The peptide bond has two resonance forms

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17
Q

Why rotation around N-Ca-C is restricted

A

Rotation around N-Ca-C is restricted due to steric constraints

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18
Q

The four levels of protein structure

A

Primary Structure

Secondary Structure

Tertiary Structure

Quaternary Structure

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19
Q

Definition of the secondary structure of proteins

A

The spatial arrangement of the polypeptides backbone

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20
Q

How the a-helix is specifically formed, stabilized, and ways to represent it

A

There are 3.6 amino acid residues in the helix.

H-bonds along the helical axis stabilize this structure

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21
Q

How the b-pleated sheet is specifically formed, stabilized, and ways to represent it

A

beta-pleated sheets are antiparallel and are extended compared to the double helix. Beta strands can be connected by turns or loops.

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22
Q

How the beta strands can be connected to form sheets

A

Colinear H-bonds create stability

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23
Q

How are B strands connected through H-bonds on the B sheet?

A

Beta strands can be connected by turns or loops of stabilizing H-bonds with irregular secondary structures. Antiparallel beta sheets are easily connected

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24
Q

Distinguish parallel and anti-parallel b-sheets

A

Parallel beta-sheet strands run up the same way starting with carbon and ending with nitrogen. Antiparallel beta-sheet strands run opposite to each other

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25
Q

Which beta sheet type is more stable and why

A

Antiparallel because the colinear H bonds create stability and are easily connected

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26
Q

How proteins differ in their composition

A

Proteins differ in their composition by the number of amino acid residues. The normal range of the number of amino acid residues is 153 (myoglobin) - 416 (phosphorylase kinase (yeast)).

(#AA residues)(110)=Molar mass

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27
Q

Definition of 3o structure of proteins, ways to represent it, and their advantages

A

The tertiary structure is the overall three-dimensional structure of a polypeptide made of interactions between the R-groups of the amino acids that make up the protein.

Tertiary structures have hydrophobic interactions, in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules.

There’s one special type of covalent bond that can contribute to tertiary structure: the disulfide bond. Disulfide bonds, covalent linkages between the sulfur-containing side chains of cysteines, are much stronger than the other types of bonds that contribute to tertiary structure. They act like molecular “safety pins,” keeping parts of the polypeptide firmly attached to one another.

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28
Q

Recognize protein types: all-alpha, all-beta, alpha/beta

A
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29
Q

How to identify layers in proteins and the location of non-polar residues

A

polar molecules are exterior and nonpolar molecules are on the interior or the proteins

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30
Q

Major stabilizing force of the tertiary structure

A

The largest force governing protein structure is the hydrophobic effect which causes nonpolar groups to aggregate in order to minimize their contact with water.

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31
Q

Meaning of a protein domain

A

Domain: a polypeptide segment that has folded into a single structural unit with a hydrophobic core

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32
Q

General principles of globular proteins

A
  • Typically at least 2 layers of secondary structure
  • Hydrophobic core
    • Typically rich in secondary structure
    • H-bonds minimize hydrophilicity of the polar backbone groups
  • Hydrophilic surface
    • Typically with irregular structure
    • Polar backbone groups of loops can form H-bonds with water
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33
Q

Correlation of residue’s hydrophobicity with location

A

The greater the residue’s hydrophobicity is, the more likely it is found in the interior of the protein

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34
Q

Role of ions pairs, disulfide bonds, and metals in the stabilization of proteins

A

Some proteins are stabilized by electrostatic or ionic interactions.

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35
Q

Characteristics of protein folding in vivo vs in vitro

A

In Vivo: a newly synthesized polypeptide begins to fold as it leaves the ribosome

  1. may require molecular chaperones
  2. post-translation process

In Vitro: full-length polypeptide is denatured and then allowed to renature.

  1. Not a random process
  2. Afinsen found that primary structure determines tertiary structure
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36
Q

Molecular chaperones: what they are and what they do

A

In the laboratory, certain small proteins can be repeatedly denatured and renatured, but in the cell, protein folding is more complicated and may require the assistance of other proteins. Some of these are known as molecular chaperones

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37
Q

Anfinsen’s postulate

A

The structure of a small globular protein is determined by the protein’s amino acid sequence

38
Q

What is the driving force of protein folding

A

hydrophobic effect

39
Q

The largest stabilizing force in proteins

A

Hydrophobic effect.

H-bonding is NOT a major determinant of protein stability

40
Q

How to interpret the folding funnel

A

When the protein is in the unfolded state there are many forms and increased entropy. When the protein is in the folded state it has one conformation and decreased entropy.

41
Q

Definition of quaternary structure

A

The spatial arrangement of polypeptides is known as the protein’s quaternary structure.

Most proteins, especially those with molecular masses greater than 100 kD, consist of more than one polypeptide chain. The individual chains, called subunits, may all be identical, in which case the protein is known as a homodimer, homotetramer, and so on. If the chains are not all identical, the prefix hetero- is used.

The forces that hold subunits together are similar to those that determine the tertiary structures of the individual polypeptides.

42
Q

Meaning of a subunit

A

individual polypeptide chains and two or more are quarternary structures

43
Q

Nomenclature used to distinguish the different types of quaternary structure

A

The individual polypeptide chains, called subunits, may all be identical, in which case the protein is known as a homodimer, homotetramer, and so on. If the chains are not all identical, the prefix hetero- is used.

44
Q

Techniques used to separate proteins

A

Chromatography

45
Q

Separation bases of size-exclusion chromatography

A

Separation based on size. Also called gel filtration

46
Q

Other name of size-exclusion chromatography

A

gel filtration

47
Q

Separation bases of ion-exchange chromatography

A

Protein separation based on differences in net charge.

(-) charged proteins bind to (+) charged solid supports and (+) charges proteins bind to (-) charges sold supports

48
Q

Components of SDS-PAGE

A

Used to verify purification of a protein.

Separation is based on mass and size

49
Q

Separation bases of SDS-PAGE

A

BetaME is added to reduce disulfide bonds. SDS is added to denature protein and add a (-) charge. 1 SDS bonds uniformly along the chain every 2 amino acid residues and the protein is separated on the basis of mass or size.

50
Q
A

D. Asp

51
Q
A

B

52
Q
A

D. Asp

53
Q
A

B. His

54
Q
A

D. Polar Neutral

55
Q
A

B. Acidic

56
Q
A

C. Tyr

57
Q
A

C. T N Y

58
Q
A

B. +1

59
Q
A

D. Cys

60
Q
A

E. W, Y, F

61
Q
A

E. W

62
Q
A

C. Glu

63
Q
A

E. His

64
Q
A

E. L & W

65
Q
A

B. b

66
Q
A

C. A pentapeptide with 4 peptide bonds

67
Q
A

E. 5

68
Q
A

B. -1

69
Q
A

E. +2

70
Q
A
71
Q
A

A. a

72
Q
A

C. 5

18/3.6=5

73
Q
A

C. It is not stabilized by the H-bonds

74
Q
A

A. Alpha helix

75
Q
A

D. An anitparallel Beta sheet

76
Q
A

C. Parallel beta sheets are more stable than anti-parallel ones

77
Q
A

C. The protein’s amino acid sequence (primary structure)

78
Q
A

B. Disulfide bond

79
Q
A

E. Hydrophobic interactions

80
Q
A

B. The tendency of non-polar molecules to avoid interaction with water and thus aggregate

81
Q
A

C. Leu; Ser

82
Q
A

C. Glu (-) - Asn - Ser - Thr - Arg (+)

83
Q
A

C. E (glutamate)

84
Q
A

B. His; H-bond

Ser is polar nuetral

85
Q

What is the abbreviated form of hemoglobin?

A

alpha2beta2

86
Q

What are the 3 most commonly used types of chromatography?

A
  1. Ion-exchange chromatography
  2. Gel-filtration chromatography
  3. Affinity chromatography
87
Q
A

D. Gel-filtration chromatography

88
Q
A

E. All of the above

89
Q
A

B. Largest

90
Q
A

B. Size

91
Q
A

E. Lysozyme, hemoglobin, TPI

92
Q
A

D. Hemoglobin, TPI, myoglobin, lysozyme

XX. BioChemistry (15 decks)

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