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BCH451 > Chapter 4: The 3D Structure of Proteins > Flashcards

Chapter 4: The 3D Structure of Proteins Flashcards

1
Q

What is a protein’s specific three-dimensional conformation?

A

its native fold

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2
Q

Why are native folds important for proteins?

A

allow for a large number of favorable interactions

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3
Q

What is the cost associated with folding a protein into its native fold?

A

cost in conformational entropy

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4
Q

What is generally true about the Gibbs free energy of proteins?

A

they have the lowest Gibbs free energy

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5
Q

What allows a protein’s native fold to fulfill biological function?

A

its structure

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6
Q

What does water make the best hydrogen bonds with?

A

itself

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7
Q

Where are van der Waals forces the most important in a protein?

A

in its interior

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8
Q

Types of favorable interactions in proteins? (5)

A

hydrophobic effect, van der Waals, hydrogen bonds, ionic interactions, disulfide bridges

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9
Q

What type of interaction leads to a-helices and b-sheets?

A

hydrogen bonds

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10
Q

Why are hydrogen bonds maximized in a protein structures?

A

allows polar molecules to easily traverse the interior of proteins

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11
Q

Describe ionic interactions.

A

long-range strong interactions between permanently charged groups

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12
Q

What type of interaction are salt-bridges?

A

ionic interactions

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13
Q

Where are salt-bridges most used for stabalization?

A

in hydrophobic environments

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14
Q

In what types of proteins are disulfide bridges generally found in?

A

secreted proteins; they don’t like the reducing environment of the cell

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15
Q

What drives the hydrophobic effect?

A

entropy!

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16
Q

What type of standard chemical interaction are disulfide bridges?

A

covalent bonding

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17
Q

Why does entropy drive the hydrophobic effect?

A

when hydrophobic molecules group up, water molecules are displaced –> increasing entropy

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18
Q

Does there exist an attractive force between two nonpolar molecules?

A

no! water pushes them together

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19
Q

Since water pushes nonpolar molecules together, what type of bond influences the hydrophobic effect?

A

hydrogen bonds

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20
Q

What creates the hydrophobic core of most proteins?

A

the burial of hydrophobic side chains in the interior of the protein; polar side chains remain exposed to water

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21
Q

Where are ionic interactions strongest?

A

in hydrophobic environments with a low dielectric constant

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22
Q

Where are ionic interactions weakest?

A

in aqueous or solvent exposed locations

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23
Q

A low dielectric constant is associated with what type of environment?

A

a hydrophobic environment

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24
Q

What is the weakest interaction in proteins?

A

van der Waals forces

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25
Q

What is the strength of van der Waals forces (kj/mol)

A

2-4 kj/mol

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26
Q

What types of atoms are van der Waals forces present?

A

in all atoms!

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27
Q

What are the two types of van der Waals forces?

A

london dispersion and steric repulsion

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28
Q

Is london dispersion an attractive or repulsive force?

A

attractive

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29
Q

What type of van der Waals force dominates at longer distances?

A

london dispersion

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30
Q

What type of van der Waals force dominates are shorter distances?

A

steric repulsion

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31
Q

What does steric repulsion depend upon?

A

the size of the atoms

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32
Q

What are london dispersion forces caused by?

A

instantaneous polarization due to fluctuating charge disributions

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33
Q

What is the van der Waals radius?

A

the specific distance where attractive and repulsive forces balance

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34
Q

What does the van der Waals radius depend the most on?

A

an atom’s size

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35
Q

On a graph of the van der Waals radius, what are the x and y components?

A

x: distance between two atoms y: energy

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36
Q

Where, on a graph of van der Waals radius, is there the strongest attraction?

A

at the lowest point aka the van der Waals contact distance

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37
Q

Why is the reversibility of weak bonds essential in cellular biochemistry?

A

binding of substrates

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38
Q

Describe the two conditions of weak bonds that make them so effective.

A

reversibility and complementary

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39
Q

Why is it important for binding surfaces to be complementary?

A

allows for multiple binding interactions

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40
Q

What are the basics of a proteins primary structure?

A

amino acid residues

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41
Q

What are the four levels of protein structure?

A

primary, secondary, tertiary, quaternary

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42
Q

What are the basics of a protein’s secondary structure?

A

a-helix or b-sheet

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43
Q

What are the basics of a protein’s tertiary structure?

A

polypeptide chains; interactions of R groups

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44
Q

What are the basics of a protein’s quaternary structure?

A

assembled subunits

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45
Q

What is the most important bond in influence the structure of a protein?

A

peptide bonds

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46
Q

Peptide bonds are what type of bond?

A

partial double bonds

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47
Q

Describe characteristics of a peptide bond. (3)

A

rigid, nearly planar, and mostly in trans conformations due to steric hinderance

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48
Q

What conformation (cis/trans) is favored in peptide bonds?

A

trans (>99.95%)

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49
Q

What amino acid is the one exception to the trans conformation rule?

A

proline; found ~6% in cis conformation via proline isomerases

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50
Q

Can a there be rotation around the peptide bond? What about the other bonds connected to the alpha carbon?

A

peptide bonds CANNOT rotate, the other bonds connected to the alpha carbon are permitted to rotate

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51
Q

What is the phi bond angle?

A

the rotation of the bond from the alpha carbon to nitrogen

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52
Q

What is the psi bond angle?

A

the rotation of the bond from the alpha carbon to the carbonyl

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53
Q

Why are some phi and psi bond combinations very unfavorable?

A

steric crowding

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54
Q

Why are some phi and psi bond combinations favorable?

A

favorable hydrogen bonding interactions along the backbone

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55
Q

What is a Ramachandran plot?

A

a plot of phi and psi bond angles calculated based upon known atomic radii and bond lengths

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56
Q

What is the purpose of a Ramachandran plot?

A

used to show “allowed” phi and psi conformations

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57
Q

What is the term for the local spatial arrangement of the polypeptide backbone?

A

secondary structures

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58
Q

What are the two most common secondary structures?

A

a-helix and b-sheet

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59
Q

What are irregular arrangements of the polypeptide chain called?

A

random coil

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60
Q

What stabilizes an a-helix? What residues are involved?

A

hydrogen bonds between nearby residues

61
Q

What percentage of amino acids are in the a-helix conformation?

A

25%

62
Q

What stabalizes a b-sheet? What residues are involved?

A

hydrogen bonds between adjacent residues that may be far away

63
Q

Are a-helixes and b-sheets the only type of secondary structures?

A

No, but they are the most prevelent

64
Q

What is the helical backbone held together by?

A

hydrogen bonds

65
Q

What amino acids make up the helical backbone?

A

n and n+4 amino acids

66
Q

Are a-helixes right or left handed?

A

right-handed

67
Q

How many residues per turn of the alpha helix?

A

3.6

68
Q

Are peptide bonds perpendicular or parallel to the helical axis?

A

parallel

69
Q

Are side chains perpendicular or parallel to the helical axis?

A

perpendicular, to reduce steric hinderance

70
Q

What is the size of the inner diameter of the a-helix? Why is this significant?

A

4-5 angstroms; its too small for anything to fit inside of

71
Q

What is the size of the outer diameter of the a-helix? Why is this significant?

A

10-12 angstroms; it fits well into the major groove of dsDNA (the perfect size!)

72
Q

What residues align on top of each other when looking down an a-helix?

A

residues 1 and 8

73
Q

Can all polypeptide sequences adopt a-helical structures?

A

Nope

74
Q

What amino acids are strong helix formers?

A

small hydrophobic residues like Alanine and Leucine

75
Q

What amino acids are strong helix breakers?

A

Proline and Glycine

76
Q

Why is proline a helix breaker?

A

rotation around the N-C bond is impossible

77
Q

Why is glycine a helix breaker?

A

the tiny R-group is too flexible, supports other conformations

78
Q

In addition to specific amino acids, what else can affect the formation of an a-helix?

A

the attractive or repulsive interactions between side chains that are 3-4 amino acids apart

79
Q

What type of side chains that are 3-4 amino acids apart will cause helical instability?

A

negative-negative, positive-positive, bulky residues

80
Q

Why might negatively charged residues occur often at one end of the helix?

A

peptide bonds have strong dipole moments that can create a partial positive amino terminus and a partial negative carboxyl terminus

81
Q

Describe the structure of b-sheets?

A

pleated sheet-like structure with side chains protruding up and down from the sheet

82
Q

What is a parallel b-sheet?

A

a sheet where the H-bonded strands run in the same direction

83
Q

What is an antiparallel b-sheet?

A

a sheet where the H-bonded strands run in opposite directions

84
Q

Do antiparallel or parallel b-sheets have stronger H-bonds?

A

antiparallel, the H-bonds are linear rather than bent

85
Q

How many amino acids does it take to complete a 180° turn?

A

four amino acids

86
Q

What stabilizes a beta turn?

A

a hydrogen bond from the carbonyl oxygen to the amide proton of a residue three down

87
Q

What amino acids are common in beta turns?

A

proline (cis) and glycine

88
Q

What type of analysis is used in the lab to investigate the secondary structure of proteins?

A

CD spectroscopy

89
Q

Can proteins be 100% a-helix or 100% b-sheet?

A

yes! but most are some combination of the two

90
Q

What is the overall spatial arrangment of atoms in a protein called?

A

tertiary structure

91
Q

What are the two major classes of tertiary structures?

A

fibrous and globular

92
Q

What are motifs/folds?

A

small combinations that are associated with a specific function; rely on their environment for stability and cannot fold by themselves

93
Q

What is a protein domain?

A

a part of a polypeptide chain that is independently stable and can fold by itself

94
Q

How many domains do small proteins usually have?

A

one domain

95
Q

What two characteristics do domains optimize?

A

burial of hydrophobic residues and satisfaction of aa sequence constraints

96
Q

What is the purpose of having more than one domain in a single protein?

A

can act as a point of regulation, can be important in catalysis (open/close)

97
Q

Are domains are motifs larger?

A

domains

98
Q

Can motifs exist outside of domains?

A

no

99
Q

Can domains exist outside of motifs?

A

yes

100
Q

Fibrous vs Globular: shape

A

long and narrow versus round and spherical

101
Q

Fibrous vs Globular: role

A

structural vs functional

102
Q

Fibrous vs Globular: solubility

A

insoluble vs soluble

103
Q

Fibrous vs Globular: sequence

A

repetitive sequence vs irregular sequence

104
Q

Fibrous vs Globular: stability

A

less sensitive vs more senstivie

105
Q

What are some common examples of fibrous proteins?

A

collagen and keratin

106
Q

What are some common examples of globular proteins?

A

catalase and insulin

107
Q

Scurvy is caused due to a deficiency in vitamin C that impacts collagen productive. Explain.

A

The hydroxylation of proline is required for collagen structure. This process converts Fe2+ –> Fe3+. Ascorbate (vitamin c) is required to convert Fe3+ —> Fe2+ to be used again.

108
Q

What are the causes of brittle bone disease and loose joints?

A

amino acid substitutions of a single glycine for larger amino acids; prevents proteins from being as tightly packed together

109
Q

What are the functions of globular proteins (6)?

A

catalysis, transport, storage, structure/movement, transmission of messages, defense

110
Q

What is a common type of transport protein?

A

hemoglobin

111
Q

What is a common type of storage protein?

A

myoglobin

112
Q

What is a common type of structure/movement proteins?

A

myosin

113
Q

What is a common type of transmission proteins?

A

insulin

114
Q

What is a common type of defense proteins?

A

antibodies and cytokines

115
Q

What is a common type of catalyst protein?

A

chymotrypsin and lysozyme

116
Q

What is the function of myoglobin? What is its structure?

A

stores oxygen and allows for consistent diffusion by contracting muscles, made up of 70% a-helix with a packed hydrophobic core

117
Q

What are intrinsically disorder proteins?

A

proteins that lack definable structure

118
Q

Why are intrinsically disordered proteins important?

A

they can conform to many different proteins, facilitating interactions with many different partners and pathways

119
Q

What are two of the well-known intrinsically disordered proteins? What are their functions?

A

p27 and p53; p27 inhibits protein kinases to stop the cell cycle

120
Q

How is the quaternary structure formed? What is another word for quaternary structure (2)?

A

by the assembly of individual polypeptides (subunits) into a larger functional cluster; multimer or oligomer

121
Q

What are the advantages of proteins having a quaternary structure (4)?

A

use the same gene and same transcription factors thus conserving space, reduces the change of mutation, speeds up translation, ensures proper folding

122
Q

How does a quaternary structure reduce mistakes and mutations?

A

can easily discard faulty subunits, no sunk cost falacy

123
Q

How does a quaternary structure make folding easier?

A

it’s easier to build up proteins, especially complex structures, from subunits

124
Q

Roughly, what is the typical speed of translation?

A

1000 amino acids in one minute

125
Q

What is it called when the use of quaternary structures increases the rate of translation?

A

parallel processing

126
Q

What is cooperativity?

A

characteristic of quaternary structures; allows the binding of one ligand to a protein to increase the affinity for future binding

127
Q

What is allostery?

A

characteristic of quaternary structures; allows the binding of one ligand to influence the binding site or function of the protein

128
Q

How does quaternary structures impact kinetics?

A

the interactions between units can change protein activity and kinetics

129
Q

What is substrate channeling?

A

characteristic of quaternary structures; when two or more enzymes interact to transfer a metabolite from one active site to another without diffusion

130
Q

What is the function of the protein albumin?

A

carries many molecules in the blood

131
Q

What is the function of the protein ferratin?

A

stores ~4500 iron (III) molecules in its core

132
Q

What is the term for the coordination of many different pathways in order to regulate protein activity?

A

proteostasis

133
Q

What two elements are required for a protein to be considered denatured?

A

the loss of its tertiary structure and accompanying loss of activity

134
Q

How can proteins be denatured (4)?

A

heat/cold, pH extremes, organic solvents, chaotropic agents that break H bonds

135
Q

Can denaturation be reversible?

A

yes! (but most used in lab are irreversible)

136
Q

What is a Tm value?

A

the point where 50% of proteins are denatured

137
Q

What is the significance of the 1972 Nobel Prize in Chemistry?

A

awarded to Christian B Anfinsen for his work concerning the connection between amino acid sequence and the functional conformation

138
Q

Describe Christian B Anfinsen’s ribonuclease refolding experiment?

A
  • ribonuclease is a small protein with four disulfide bonds
  • only one of its formations (out of 105) are functional
  • urea denatures ribonuclease
  • when urea is removed, the protein spontaneously refolds even with the correct disulfide bonds
139
Q

What did Christian B Anfinsen conclude from his experiment?

A

that the amino acid sequence ALONE determines the native conformation

140
Q

What is Levinthal’s paradox?

A

it is mathematically impossible for protein folding occur by randomly trying ever conformation until the lowest-energy one is found

141
Q

How can protein folding NOT be random?

A

direction toward the native (lowest energy) structure is always thermodynamically most favorable

142
Q

Describe the idea of a folding funnel.

A

folding properties are related to free energy and the possible conformations of a protein are reduced as it approaches native-like structure

143
Q

What is the term used to describe proteins that facilitate the folding of other proteins?

A

chaperonins

144
Q

Describe the significance of the GroEL/s chaperonin?

A

10-15% of E. coli proteins require its hydrophobic pocket to fold

145
Q

What is amyloidosis?

A

the deposition of fibrils throughout the body

146
Q

How does the cholera toxin lead to disease?

A

unfolds in the ER, is transported to the cytoplasm for degradation

147
Q

What are three disease like things caused by protein misfolding?

A

amyloidosis, cholera, and prions

148
Q

What are the three principles that determine protein conformation?

A

1) like dissolves like (nonpolar buried in nonpolar)
2) folded must be happier than unfolded (solvent entropy)
3) two atoms cannot be in the same place at once (steric hinderance

BCH451 (3 decks)

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