Chapter 4 + Quiz Questions Flashcards
(118 cards)
1
Q
What is a peptide bond?
A
Covalent linkages between amino acids
2
Q
How do peptide bonds form?
A
By condensation reactions involving the loss of a water molecule
3
Q
Formation of peptide bonds eliminates the ____, which is important for protein folding
A
Alpha-carboxyl and alpha amino charged groups
4
Q
True or False: peptide bonds are the same, independent of the amino acids being joined?
A
True
5
Q
The main chain is the ___ portion of the polypeptide, the side chains are ____
A
constant, variable
6
Q
What is the repeating pattern in the main chain?
A
NCCNCC
7
Q
Rotation around C-N peptide bond is restricted due to?
A
Its partial double-bond characteristic
8
Q
As a consequence of the partial double bond characteristic, the six atoms of the peptide group are ___ and ___
A
rigid and planar
9
Q
The partial double bond of the peptide bond creates?
A
Cis-trans isomers
10
Q
The oxygen of the carbonyl group and the hydrogen of the amide nitrogen are usually ___ to each other
A
trans
11
Q
Define steric exclusion
A
Two groups can’t occupy the same space at the same time
12
Q
Why is the trans configuration favored over the cis configuration?
A
The cis configuration is more likely to cause steric interference
13
Q
What are the four levels of protein structure?
A
Primary, Secondary, Tertiary, Quaternary structure
14
Q
What is the primary structure?
A
Defines the linear arrangement of amino acids in a polypeptide. Contains the information specifying correct folding
15
Q
How is the primary structure presented?
A
From the N (amino) terminus to the C (carboxyl) terminus
16
Q
True or False: it is not yet possible to reliably predict three-dimensional structure based on primary structure?
A
True
17
Q
How is the primary structure often determined?
A
Through investigation of the corresponding gene
18
Q
What is the secondary structure?
A
Representation of localized patterns of folding in a polypeptide
19
Q
How is the secondary structure maintained?
A
By hydrogen bonds between main-chain amide and carbonyl groups
20
Q
What kind of structure are alpha-helicies and beta-sheets considered?
A
Secondary
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
22
Q
Secondary structures retain the same overall characteristics ____ of the protein context
A
independent
23
Q
Viable forms of secondary structure have two key rules, what are they?
A
- Optimize the hydrogen bonding potential of main-chain carbonyl and amide groups
- Represent a favored conformation of the polypeptide chain
24
Q
Each peptide bond has a ____donor and acceptor groups
A
hydrogen bond
25
True or False: there is an odd number of hydrogen bond donors and acceptors within the polypeptide main chain?
False: there is an equal number of hydrogen bond donors and acceptors within the polypeptide main-chain
26
Why is the fact that there is an equal number of hydrogen bond donors and acceptors within the polypeptide main-chain important?
It optimizes hydrogen bonds
27
Each alpha-carbon is held within the main-chain through what kind of bond? What does this mean for rotation?
Held through single-bonds, about which there is complete freedom of rotation
28
What are the two specialty bonds in secondary structures?
1. Phi, Φ, Cα-N
2. Psi, ψ, Cα-C
29
Theoretically, phi and psi can each range from ___ to ___
-180 to 180
30
What prevents the formation of most conformations?
Steric Interference
31
What plots illustrate the possible combinations of phi and psi? And describe it.
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
32
What is an α-Helix?
A right-handed helix with 3.6 residues/turn
33
How are α-helices stabilized?
By hydrogen bonds which run parallel to the axis of the helix
34
The carbonyl groups point towards the __-terminus; amide groups to the __-terminus
C, N
35
Each carbonyl of residue __ hydrogen bonds with amide group of reside ___
n, n+4
36
Which amino acid, because of its rigidity, is not usually found in α-helices?
Proline
37
Which amino acid, because of its flexibility, is also uncommon in α-helices?
Glycine
38
Amino acids with _______ are less common due to steric interference. Which are these amino acids?
Side chain branches. This includes valine, threonine, and isoleucine
39
Amino acids with _____ groups near the main-chain are also less common. Which are these amino acids?
Hydrogen bonding groups, This includes serine, aspartate, and asparagine
40
Charged residues tend to be positions to form ____ pairs
Favorable ion
41
True or False: every peptide bond has a small electrical dipole
True
42
Each dipole communicated through helix by hydrogen bonding gives the helix a ..?
Net dipole
43
N terminus has a partial ___ dipole charge
C terminus has a partial ___ dipole charge
+, -
44
How is the dipole stabilized in a helix?
By residues at each termini whose charge opposes the helix dipole
45
__ charged residues at the N terminus
__ charged residues at the C terminus
-, +
46
Which amino acids could be found at the N terminus?
Aspartate, Glutamate
47
Which amino acids could be found at the C terminus?
Lysine, Arginine, Histidine
48
What is an amphipathic helix?
The positioning of hydrophobic and hydrophilic residues within the primary structure.
49
True or False: an amphipathic helix is polar?
False, it has both polar and non-polar faces
50
Residues separated by 3 or 4 positions in the primary helix will be on the __ side of an α-helix
Same
51
Residues separated by two residues in the primary structure will be on the ____ sides of the helix
Opposite
52
What is a beta sheet?
Are made up of β strands arranged side-by-side. They often involve 4/5 strands
53
What is the conformation of a β sheet?
Fully extended polypeptide chains
54
How are β sheets stabalized?
By hydrogen bonds between C (double bond) O, and -NH on adjacent strands
55
True or False: β sheets are simultaneously parallel and anti-parallel?
False, they are either parallel or anti-parallel
56
In parallel β sheets, the strands run in the ____ direction
Same
57
In anti-parallel β sheets, the strands run in the ____ direction
Opposite
58
Why are anti-parallel β sheets more stable?
Due to better geometry of hydrogen bonding
59
What is the third kind of β sheet?
Mixed
60
What is a mixed β sheet?
Contains both parallel and antiparallel strands
61
What is an amphipathic beta sheet?
When there are alternating polar and non-polar residues within the primary structure of a beta sheet
62
True or False: in the context of beta sheets, side chains tend to alternate above and below the polypeptide chain?
True
63
What is the tertiary structure?
It represents the final folding pattern of a single polypeptide
64
What is the native conformation?
The biological active folding pattern
65
What does tertiary structure describe?
The long range aspects of sequence interactions within a polypeptide
66
Residues separated by great distance in primary structure may be in _____ in tertiary structure
close proximity
67
True or False: different proteins have different tertiary structures, which relates to their unique functions?
True
68
The tertiary structures of different proteins vary in their content of what?
Alpha helices and beta sheets
69
Define stability
The tendency to maintain a native conformation
70
True or False: proteins are incredibly stable?
False: proteins are only marginally stable
71
What kind of interactions predominate in stabilizing protein structure?
Weak interactions
72
A protein conformation with low free energy has was relationship with stability?
Low free energy generally means more stable
73
The protein conformation with the lowest free energy is usually the one with the _____ number of weal interactions
maximum
74
What does the stability of a protein reflect?
The difference in the free energies of the folded and unfolded state
75
Is protein folding a slow or rapid process?
Rapid
76
Since protein folding is a rapid process, what does this mean for folding patterns?
It means that proteins don't sample all possible folding patterns
77
Which analogy can be used to visualize protein folding, and what is said analogy?
It can be imagined as a funnel where a large number or unstable conformations collapse to a single, stable folding pattern
78
True or False: all proteins spontaneously fold to their native conformations?
False: some proteins fold to their native conformations, others require the help of chaperones
79
What is a chaperone in protein folding?
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
What is denaturation?
The disruption of native conformation with loss of biological activity
81
How much energy is required for denaturation?
Often a small amount, only a few hydrogen bonds
82
Protein folding and denaturation is a _____ process
cooperative
83
For many proteins, is denaturation reversible?
Yes
84
Does quaternary structure have to involve multiple subunits of the same polypeptide?
No, it can be of the same polypeptide or different polypeptides
85
Subunits usually associate through ______ interactions
Non-covalent
86
What are some biological advantages associated with quaternary structure?
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
What are 7 different biological roles of proteins?
Enzymes, Storage and Transport, Physical cell support and shape, Mechanical movement, decoding cell information, hormones and hormone receptors, other specialized functions
88
Why is insulin often used as the threshold of when a polypeptide becomes a protein?
Because its length is 51 acids
89
How would you calculate the number of amino acids is a protein?
Dividing the proteins molecular weight by 110
90
The three dimensional structure of a protein is determined by its..?
Amino acid sequence
91
Which forces are the most important in stabilizing protein structure?
Non-covalent
92
What are the 3 fibrous proteins?
Keratin, Collagen, and Silk
93
What are the 2 golbular proteins?
Myoglobin and Hemoglobin
94
At the level of primary structure keratin contains a ________ where position a and d are hydrophobic residues ( a b c d e f g )
pseudo-seven repeat
95
At the level of secondary structure, keratin forms ____
An alpha-helix
96
Residues from positions "a" and "d" end up on the same face of the helix, resulting in what?
A hydrophobic strip along the length of the helix
97
What is a coiled coil?
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
The coiled-coil of keratin involves two ____ _____ helices wrapping around each other in a left-handed fashion
right-handed
99
Where does keratin get its strength?
From covalent linkages of individual units into higher-order structures. These individual units are linked together through disulfide bonds.
100
The extent of the disulfide bonding will determine the ___ of the overall keratin structure
strength
101
At the level of primary structure, collagen contains repeats of Gly-X-Y where X is often..?
proline
102
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
left-handed
103
___ left-handed helices of collagen come together to form a coiled-coil
3
104
In collagen, 3 left-handed helices wrap around each other in a ___-___ fashion
right-handed
105
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
outside, inside
106
Where does collagen get its strength?
From covalent linkages between the individual units into higher order structures; but not from disulfides, instead from residues that undergo post-translational modifications
107
The covalent crosslinks of collagen involve ___-____ modified residues
post-translationally
108
The enzymes performing these modifications in collagen require what vitamin? What happens without these modified residues?
Vitamin C. Without them, collagen cannot form the stabilizing crosslinks
109
What is an example of collagen being unable to form these crosslinks?
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
At the level of primary structure, most silk has a ___ residue repeat
(GSGAGA) (GSGAGA) (GSGAGA)
6
111
At the level of secondary structure, silk is composed primarily from what?
beta-sheets
112
The fully extended polypeptides offer considerable strength. On a cross sectional basis ___ is one of the strongest known materials
silk
113
What aspects of silk's structure helps conceptualize the basis of its strength and flexibility?
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
The strength of silk arises as a consequence of..?
fully extended polypeptide chains
115
The amino acid residues of a polypeptide chain are linked together through..?
peptide bonds
116
True or False: tertiary structure represents the final folding pattern of a single polypeptide chain?
True
117
Keratin is similar to collagen in that they both..?
have repeating patterns at the level of primary structure
118
Which of these functional groups is ABSENT from the peptide SKCH?
Guanidino
