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BMSC 200 > Chapter 4 + Quiz Questions > Flashcards

Chapter 4 + Quiz Questions Flashcards

1
Q

What is a peptide bond?

A

Covalent linkages between amino acids

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2
Q

How do peptide bonds form?

A

By condensation reactions involving the loss of a water molecule

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3
Q

Formation of peptide bonds eliminates the ____, which is important for protein folding

A

Alpha-carboxyl and alpha amino charged groups

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4
Q

True or False: peptide bonds are the same, independent of the amino acids being joined?

A

True

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5
Q

The main chain is the ___ portion of the polypeptide, the side chains are ____

A

constant, variable

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6
Q

What is the repeating pattern in the main chain?

A

NCCNCC

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7
Q

Rotation around C-N peptide bond is restricted due to?

A

Its partial double-bond characteristic

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8
Q

As a consequence of the partial double bond characteristic, the six atoms of the peptide group are ___ and ___

A

rigid and planar

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9
Q

The partial double bond of the peptide bond creates?

A

Cis-trans isomers

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10
Q

The oxygen of the carbonyl group and the hydrogen of the amide nitrogen are usually ___ to each other

A

trans

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11
Q

Define steric exclusion

A

Two groups can’t occupy the same space at the same time

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12
Q

Why is the trans configuration favored over the cis configuration?

A

The cis configuration is more likely to cause steric interference

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13
Q

What are the four levels of protein structure?

A

Primary, Secondary, Tertiary, Quaternary structure

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14
Q

What is the primary structure?

A

Defines the linear arrangement of amino acids in a polypeptide. Contains the information specifying correct folding

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15
Q

How is the primary structure presented?

A

From the N (amino) terminus to the C (carboxyl) terminus

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16
Q

True or False: it is not yet possible to reliably predict three-dimensional structure based on primary structure?

A

True

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17
Q

How is the primary structure often determined?

A

Through investigation of the corresponding gene

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18
Q

What is the secondary structure?

A

Representation of localized patterns of folding in a polypeptide

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19
Q

How is the secondary structure maintained?

A

By hydrogen bonds between main-chain amide and carbonyl groups

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20
Q

What kind of structure are alpha-helicies and beta-sheets considered?

A

Secondary

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21
Q

True or False: elements of secondary structure are not found in different proteins?

A

False, elements of secondary structure are found in different proteins

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22
Q

Secondary structures retain the same overall characteristics ____ of the protein context

A

independent

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23
Q

Viable forms of secondary structure have two key rules, what are they?

A
  1. Optimize the hydrogen bonding potential of main-chain carbonyl and amide groups
  2. Represent a favored conformation of the polypeptide chain
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24
Q

Each peptide bond has a ____donor and acceptor groups

A

hydrogen bond

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25
Q

True or False: there is an odd number of hydrogen bond donors and acceptors within the polypeptide main chain?

A

False: there is an equal number of hydrogen bond donors and acceptors within the polypeptide main-chain

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26
Q

Why is the fact that there is an equal number of hydrogen bond donors and acceptors within the polypeptide main-chain important?

A

It optimizes hydrogen bonds

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27
Q

Each alpha-carbon is held within the main-chain through what kind of bond? What does this mean for rotation?

A

Held through single-bonds, about which there is complete freedom of rotation

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28
Q

What are the two specialty bonds in secondary structures?

A
  1. Phi, Φ, Cα-N
  2. Psi, ψ, Cα-C
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29
Q

Theoretically, phi and psi can each range from ___ to ___

A

-180 to 180

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30
Q

What prevents the formation of most conformations?

A

Steric Interference

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31
Q

What plots illustrate the possible combinations of phi and psi? And describe it.

A

Ramachadran plots, where combinations of phi and psi that are actually observed in proteins are highlighted. The favored conformations correspond to the common elements of secondary structures

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32
Q

What is an α-Helix?

A

A right-handed helix with 3.6 residues/turn

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33
Q

How are α-helices stabilized?

A

By hydrogen bonds which run parallel to the axis of the helix

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34
Q

The carbonyl groups point towards the __-terminus; amide groups to the __-terminus

A

C, N

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35
Q

Each carbonyl of residue __ hydrogen bonds with amide group of reside ___

A

n, n+4

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36
Q

Which amino acid, because of its rigidity, is not usually found in α-helices?

A

Proline

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37
Q

Which amino acid, because of its flexibility, is also uncommon in α-helices?

A

Glycine

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38
Q

Amino acids with _______ are less common due to steric interference. Which are these amino acids?

A

Side chain branches. This includes valine, threonine, and isoleucine

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39
Q

Amino acids with _____ groups near the main-chain are also less common. Which are these amino acids?

A

Hydrogen bonding groups, This includes serine, aspartate, and asparagine

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40
Q

Charged residues tend to be positions to form ____ pairs

A

Favorable ion

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41
Q

True or False: every peptide bond has a small electrical dipole

A

True

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42
Q

Each dipole communicated through helix by hydrogen bonding gives the helix a ..?

A

Net dipole

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43
Q

N terminus has a partial ___ dipole charge
C terminus has a partial ___ dipole charge

A

+, -

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44
Q

How is the dipole stabilized in a helix?

A

By residues at each termini whose charge opposes the helix dipole

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45
Q

__ charged residues at the N terminus
__ charged residues at the C terminus

A

-, +

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46
Q

Which amino acids could be found at the N terminus?

A

Aspartate, Glutamate

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47
Q

Which amino acids could be found at the C terminus?

A

Lysine, Arginine, Histidine

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48
Q

What is an amphipathic helix?

A

The positioning of hydrophobic and hydrophilic residues within the primary structure.

49
Q

True or False: an amphipathic helix is polar?

A

False, it has both polar and non-polar faces

50
Q

Residues separated by 3 or 4 positions in the primary helix will be on the __ side of an α-helix

A

Same

51
Q

Residues separated by two residues in the primary structure will be on the ____ sides of the helix

A

Opposite

52
Q

What is a beta sheet?

A

Are made up of β strands arranged side-by-side. They often involve 4/5 strands

53
Q

What is the conformation of a β sheet?

A

Fully extended polypeptide chains

54
Q

How are β sheets stabalized?

A

By hydrogen bonds between C (double bond) O, and -NH on adjacent strands

55
Q

True or False: β sheets are simultaneously parallel and anti-parallel?

A

False, they are either parallel or anti-parallel

56
Q

In parallel β sheets, the strands run in the ____ direction

A

Same

57
Q

In anti-parallel β sheets, the strands run in the ____ direction

A

Opposite

58
Q

Why are anti-parallel β sheets more stable?

A

Due to better geometry of hydrogen bonding

59
Q

What is the third kind of β sheet?

A

Mixed

60
Q

What is a mixed β sheet?

A

Contains both parallel and antiparallel strands

61
Q

What is an amphipathic beta sheet?

A

When there are alternating polar and non-polar residues within the primary structure of a beta sheet

62
Q

True or False: in the context of beta sheets, side chains tend to alternate above and below the polypeptide chain?

A

True

63
Q

What is the tertiary structure?

A

It represents the final folding pattern of a single polypeptide

64
Q

What is the native conformation?

A

The biological active folding pattern

65
Q

What does tertiary structure describe?

A

The long range aspects of sequence interactions within a polypeptide

66
Q

Residues separated by great distance in primary structure may be in _____ in tertiary structure

A

close proximity

67
Q

True or False: different proteins have different tertiary structures, which relates to their unique functions?

A

True

68
Q

The tertiary structures of different proteins vary in their content of what?

A

Alpha helices and beta sheets

69
Q

Define stability

A

The tendency to maintain a native conformation

70
Q

True or False: proteins are incredibly stable?

A

False: proteins are only marginally stable

71
Q

What kind of interactions predominate in stabilizing protein structure?

A

Weak interactions

72
Q

A protein conformation with low free energy has was relationship with stability?

A

Low free energy generally means more stable

73
Q

The protein conformation with the lowest free energy is usually the one with the _____ number of weal interactions

A

maximum

74
Q

What does the stability of a protein reflect?

A

The difference in the free energies of the folded and unfolded state

75
Q

Is protein folding a slow or rapid process?

A

Rapid

76
Q

Since protein folding is a rapid process, what does this mean for folding patterns?

A

It means that proteins don’t sample all possible folding patterns

77
Q

Which analogy can be used to visualize protein folding, and what is said analogy?

A

It can be imagined as a funnel where a large number or unstable conformations collapse to a single, stable folding pattern

78
Q

True or False: all proteins spontaneously fold to their native conformations?

A

False: some proteins fold to their native conformations, others require the help of chaperones

79
Q

What is a chaperone in protein folding?

A

Chaperones are proteins that aid in the proper folding of other proteins by facilitating their assembly without being a part of the resulting complex

80
Q

What is denaturation?

A

The disruption of native conformation with loss of biological activity

81
Q

How much energy is required for denaturation?

A

Often a small amount, only a few hydrogen bonds

82
Q

Protein folding and denaturation is a _____ process

A

cooperative

83
Q

For many proteins, is denaturation reversible?

A

Yes

84
Q

Does quaternary structure have to involve multiple subunits of the same polypeptide?

A

No, it can be of the same polypeptide or different polypeptides

85
Q

Subunits usually associate through ______ interactions

A

Non-covalent

86
Q

What are some biological advantages associated with quaternary structure?

A
  1. Helps stabilize subunits and prolong protein life
  2. Unique active sites are produced
  3. Help facilitate unique and dynamic combinations of structure/function through physiological changes in structure
  4. Conservation of functional subunits
87
Q

What are 7 different biological roles of proteins?

A

Enzymes, Storage and Transport, Physical cell support and shape, Mechanical movement, decoding cell information, hormones and hormone receptors, other specialized functions

88
Q

Why is insulin often used as the threshold of when a polypeptide becomes a protein?

A

Because its length is 51 acids

89
Q

How would you calculate the number of amino acids is a protein?

A

Dividing the proteins molecular weight by 110

90
Q

The three dimensional structure of a protein is determined by its..?

A

Amino acid sequence

91
Q

Which forces are the most important in stabilizing protein structure?

A

Non-covalent

92
Q

What are the 3 fibrous proteins?

A

Keratin, Collagen, and Silk

93
Q

What are the 2 golbular proteins?

A

Myoglobin and Hemoglobin

94
Q

At the level of primary structure keratin contains a ________ where position a and d are hydrophobic residues ( a b c d e f g )

A

pseudo-seven repeat

95
Q

At the level of secondary structure, keratin forms ____

A

An alpha-helix

96
Q

Residues from positions “a” and “d” end up on the same face of the helix, resulting in what?

A

A hydrophobic strip along the length of the helix

97
Q

What is a coiled coil?

A

When two amphipathic helices of keratin interact to bury their hydrophobic faces together. Two or more helices entwine to form a more stable structure

98
Q

The coiled-coil of keratin involves two ____ _____ helices wrapping around each other in a left-handed fashion

A

right-handed

99
Q

Where does keratin get its strength?

A

From covalent linkages of individual units into higher-order structures. These individual units are linked together through disulfide bonds.

100
Q

The extent of the disulfide bonding will determine the ___ of the overall keratin structure

A

strength

101
Q

At the level of primary structure, collagen contains repeats of Gly-X-Y where X is often..?

A

proline

102
Q

At the level of secondary structure, collagen form a ____ ___ helix of three residues per turn, as opposed to the 3.6 residues/turn of an alpha-helix

A

left-handed

103
Q

___ left-handed helices of collagen come together to form a coiled-coil

A

3

104
Q

In collagen, 3 left-handed helices wrap around each other in a ___-___ fashion

A

right-handed

105
Q

The bulky side chains of proline are on the ___ of the coiled-coil; whereas the small side chains of the glycine are on the ___ of the coiled-coil

A

outside, inside

106
Q

Where does collagen get its strength?

A

From covalent linkages between the individual units into higher order structures; but not from disulfides, instead from residues that undergo post-translational modifications

107
Q

The covalent crosslinks of collagen involve ___-____ modified residues

A

post-translationally

108
Q

The enzymes performing these modifications in collagen require what vitamin? What happens without these modified residues?

A

Vitamin C. Without them, collagen cannot form the stabilizing crosslinks

109
Q

What is an example of collagen being unable to form these crosslinks?

A

Scurvy, which is a vitamin c deficiency condition that is a result of weakened collagen, which can manifest as skin lesions, fragile blood vessels, and bleeding gums

110
Q

At the level of primary structure, most silk has a ___ residue repeat
(GSGAGA) (GSGAGA) (GSGAGA)

A

6

111
Q

At the level of secondary structure, silk is composed primarily from what?

A

beta-sheets

112
Q

The fully extended polypeptides offer considerable strength. On a cross sectional basis ___ is one of the strongest known materials

A

silk

113
Q

What aspects of silk’s structure helps conceptualize the basis of its strength and flexibility?

A
  1. Fully extended polypeptides help with strength
  2. The association of strands by hydrogen bonding help with flexibility
  3. The association of sheets by Van der Waals and hydrophobic interactions help with flexibility
114
Q

The strength of silk arises as a consequence of..?

A

fully extended polypeptide chains

115
Q

The amino acid residues of a polypeptide chain are linked together through..?

A

peptide bonds

116
Q

True or False: tertiary structure represents the final folding pattern of a single polypeptide chain?

A

True

117
Q

Keratin is similar to collagen in that they both..?

A

have repeating patterns at the level of primary structure

118
Q

Which of these functional groups is ABSENT from the peptide SKCH?

A

Guanidino

BMSC 200 (11 decks)

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