Chapter 4: The 3D Structure of Proteins Flashcards
1
Q
What is a protein’s specific three-dimensional conformation?
A
its native fold
2
Q
Why are native folds important for proteins?
A
allow for a large number of favorable interactions
3
Q
What is the cost associated with folding a protein into its native fold?
A
cost in conformational entropy
4
Q
What is generally true about the Gibbs free energy of proteins?
A
they have the lowest Gibbs free energy
5
Q
What allows a protein’s native fold to fulfill biological function?
A
its structure
6
Q
What does water make the best hydrogen bonds with?
A
itself
7
Q
Where are van der Waals forces the most important in a protein?
A
in its interior
8
Q
Types of favorable interactions in proteins? (5)
A
hydrophobic effect, van der Waals, hydrogen bonds, ionic interactions, disulfide bridges
9
Q
What type of interaction leads to a-helices and b-sheets?
A
hydrogen bonds
10
Q
Why are hydrogen bonds maximized in a protein structures?
A
allows polar molecules to easily traverse the interior of proteins
11
Q
Describe ionic interactions.
A
long-range strong interactions between permanently charged groups
12
Q
What type of interaction are salt-bridges?
A
ionic interactions
13
Q
Where are salt-bridges most used for stabalization?
A
in hydrophobic environments
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
15
Q
What drives the hydrophobic effect?
A
entropy!
16
Q
What type of standard chemical interaction are disulfide bridges?
A
covalent bonding
17
Q
Why does entropy drive the hydrophobic effect?
A
when hydrophobic molecules group up, water molecules are displaced –> increasing entropy
18
Q
Does there exist an attractive force between two nonpolar molecules?
A
no! water pushes them together
19
Q
Since water pushes nonpolar molecules together, what type of bond influences the hydrophobic effect?
A
hydrogen bonds
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
21
Q
Where are ionic interactions strongest?
A
in hydrophobic environments with a low dielectric constant
22
Q
Where are ionic interactions weakest?
A
in aqueous or solvent exposed locations
23
Q
A low dielectric constant is associated with what type of environment?
A
a hydrophobic environment
24
Q
What is the weakest interaction in proteins?
A
van der Waals forces
25
What is the strength of van der Waals forces (kj/mol)
2-4 kj/mol
26
What types of atoms are van der Waals forces present?
in all atoms!
27
What are the two types of van der Waals forces?
london dispersion and steric repulsion
28
Is london dispersion an attractive or repulsive force?
attractive
29
What type of van der Waals force dominates at longer distances?
london dispersion
30
What type of van der Waals force dominates are shorter distances?
steric repulsion
31
What does steric repulsion depend upon?
the size of the atoms
32
What are london dispersion forces caused by?
instantaneous polarization due to fluctuating charge disributions
33
What is the van der Waals radius?
the specific distance where attractive and repulsive forces balance
34
What does the van der Waals radius depend the most on?
an atom's size
35
On a graph of the van der Waals radius, what are the x and y components?
x: distance between two atoms y: energy
36
Where, on a graph of van der Waals radius, is there the strongest attraction?
at the lowest point aka the van der Waals contact distance
37
Why is the reversibility of weak bonds essential in cellular biochemistry?
binding of substrates
38
Describe the two conditions of weak bonds that make them so effective.
reversibility and complementary
39
Why is it important for binding surfaces to be complementary?
allows for multiple binding interactions
40
What are the basics of a proteins primary structure?
amino acid residues
41
What are the four levels of protein structure?
primary, secondary, tertiary, quaternary
42
What are the basics of a protein's secondary structure?
a-helix or b-sheet
43
What are the basics of a protein's tertiary structure?
polypeptide chains; interactions of R groups
44
What are the basics of a protein's quaternary structure?
assembled subunits
45
What is the most important bond in influence the structure of a protein?
peptide bonds
46
Peptide bonds are what type of bond?
partial double bonds
47
Describe characteristics of a peptide bond. (3)
rigid, nearly planar, and mostly in trans conformations due to steric hinderance
48
What conformation (cis/trans) is favored in peptide bonds?
trans (>99.95%)
49
What amino acid is the one exception to the trans conformation rule?
proline; found ~6% in cis conformation via proline isomerases
50
Can a there be rotation around the peptide bond? What about the other bonds connected to the alpha carbon?
peptide bonds CANNOT rotate, the other bonds connected to the alpha carbon are permitted to rotate
51
What is the phi bond angle?
the rotation of the bond from the alpha carbon to nitrogen
52
What is the psi bond angle?
the rotation of the bond from the alpha carbon to the carbonyl
53
Why are some phi and psi bond combinations very unfavorable?
steric crowding
54
Why are some phi and psi bond combinations favorable?
favorable hydrogen bonding interactions along the backbone
55
What is a Ramachandran plot?
a plot of phi and psi bond angles calculated based upon known atomic radii and bond lengths
56
What is the purpose of a Ramachandran plot?
used to show "allowed" phi and psi conformations
57
What is the term for the local spatial arrangement of the polypeptide backbone?
secondary structures
58
What are the two most common secondary structures?
a-helix and b-sheet
59
What are irregular arrangements of the polypeptide chain called?
random coil
60
What stabilizes an a-helix? What residues are involved?
hydrogen bonds between nearby residues
61
What percentage of amino acids are in the a-helix conformation?
25%
62
What stabalizes a b-sheet? What residues are involved?
hydrogen bonds between adjacent residues that may be far away
63
Are a-helixes and b-sheets the only type of secondary structures?
No, but they are the most prevelent
64
What is the helical backbone held together by?
hydrogen bonds
65
What amino acids make up the helical backbone?
n and n+4 amino acids
66
Are a-helixes right or left handed?
right-handed
67
How many residues per turn of the alpha helix?
3.6
68
Are peptide bonds perpendicular or parallel to the helical axis?
parallel
69
Are side chains perpendicular or parallel to the helical axis?
perpendicular, to reduce steric hinderance
70
What is the size of the inner diameter of the a-helix? Why is this significant?
4-5 angstroms; its too small for anything to fit inside of
71
What is the size of the outer diameter of the a-helix? Why is this significant?
10-12 angstroms; it fits well into the major groove of dsDNA (the perfect size!)
72
What residues align on top of each other when looking down an a-helix?
residues 1 and 8
73
Can all polypeptide sequences adopt a-helical structures?
Nope
74
What amino acids are strong helix formers?
small hydrophobic residues like Alanine and Leucine
75
What amino acids are strong helix breakers?
Proline and Glycine
76
Why is proline a helix breaker?
rotation around the N-C bond is impossible
77
Why is glycine a helix breaker?
the tiny R-group is too flexible, supports other conformations
78
In addition to specific amino acids, what else can affect the formation of an a-helix?
the attractive or repulsive interactions between side chains that are 3-4 amino acids apart
79
What type of side chains that are 3-4 amino acids apart will cause helical instability?
negative-negative, positive-positive, bulky residues
80
Why might negatively charged residues occur often at one end of the helix?
peptide bonds have strong dipole moments that can create a partial positive amino terminus and a partial negative carboxyl terminus
81
Describe the structure of b-sheets?
pleated sheet-like structure with side chains protruding up and down from the sheet
82
What is a parallel b-sheet?
a sheet where the H-bonded strands run in the same direction
83
What is an antiparallel b-sheet?
a sheet where the H-bonded strands run in opposite directions
84
Do antiparallel or parallel b-sheets have stronger H-bonds?
antiparallel, the H-bonds are linear rather than bent
85
How many amino acids does it take to complete a 180° turn?
four amino acids
86
What stabilizes a beta turn?
a hydrogen bond from the carbonyl oxygen to the amide proton of a residue three down
87
What amino acids are common in beta turns?
proline (cis) and glycine
88
What type of analysis is used in the lab to investigate the secondary structure of proteins?
CD spectroscopy
89
Can proteins be 100% a-helix or 100% b-sheet?
yes! but most are some combination of the two
90
What is the overall spatial arrangment of atoms in a protein called?
tertiary structure
91
What are the two major classes of tertiary structures?
fibrous and globular
92
What are motifs/folds?
small combinations that are associated with a specific function; rely on their environment for stability and cannot fold by themselves
93
What is a protein domain?
a part of a polypeptide chain that is independently stable and can fold by itself
94
How many domains do small proteins usually have?
one domain
95
What two characteristics do domains optimize?
burial of hydrophobic residues and satisfaction of aa sequence constraints
96
What is the purpose of having more than one domain in a single protein?
can act as a point of regulation, can be important in catalysis (open/close)
97
Are domains are motifs larger?
domains
98
Can motifs exist outside of domains?
no
99
Can domains exist outside of motifs?
yes
100
Fibrous vs Globular: shape
long and narrow versus round and spherical
101
Fibrous vs Globular: role
structural vs functional
102
Fibrous vs Globular: solubility
insoluble vs soluble
103
Fibrous vs Globular: sequence
repetitive sequence vs irregular sequence
104
Fibrous vs Globular: stability
less sensitive vs more senstivie
105
What are some common examples of fibrous proteins?
collagen and keratin
106
What are some common examples of globular proteins?
catalase and insulin
107
Scurvy is caused due to a deficiency in vitamin C that impacts collagen productive. Explain.
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
What are the causes of brittle bone disease and loose joints?
amino acid substitutions of a single glycine for larger amino acids; prevents proteins from being as tightly packed together
109
What are the functions of globular proteins (6)?
catalysis, transport, storage, structure/movement, transmission of messages, defense
110
What is a common type of transport protein?
hemoglobin
111
What is a common type of storage protein?
myoglobin
112
What is a common type of structure/movement proteins?
myosin
113
What is a common type of transmission proteins?
insulin
114
What is a common type of defense proteins?
antibodies and cytokines
115
What is a common type of catalyst protein?
chymotrypsin and lysozyme
116
What is the function of myoglobin? What is its structure?
stores oxygen and allows for consistent diffusion by contracting muscles, made up of 70% a-helix with a packed hydrophobic core
117
What are intrinsically disorder proteins?
proteins that lack definable structure
118
Why are intrinsically disordered proteins important?
they can conform to many different proteins, facilitating interactions with many different partners and pathways
119
What are two of the well-known intrinsically disordered proteins? What are their functions?
p27 and p53; p27 inhibits protein kinases to stop the cell cycle
120
How is the quaternary structure formed? What is another word for quaternary structure (2)?
by the assembly of individual polypeptides (subunits) into a larger functional cluster; multimer or oligomer
121
What are the advantages of proteins having a quaternary structure (4)?
use the same gene and same transcription factors thus conserving space, reduces the change of mutation, speeds up translation, ensures proper folding
122
How does a quaternary structure reduce mistakes and mutations?
can easily discard faulty subunits, no sunk cost falacy
123
How does a quaternary structure make folding easier?
it's easier to build up proteins, especially complex structures, from subunits
124
Roughly, what is the typical speed of translation?
1000 amino acids in one minute
125
What is it called when the use of quaternary structures increases the rate of translation?
parallel processing
126
What is cooperativity?
characteristic of quaternary structures; allows the binding of one ligand to a protein to increase the affinity for future binding
127
What is allostery?
characteristic of quaternary structures; allows the binding of one ligand to influence the binding site or function of the protein
128
How does quaternary structures impact kinetics?
the interactions between units can change protein activity and kinetics
129
What is substrate channeling?
characteristic of quaternary structures; when two or more enzymes interact to transfer a metabolite from one active site to another without diffusion
130
What is the function of the protein albumin?
carries many molecules in the blood
131
What is the function of the protein ferratin?
stores ~4500 iron (III) molecules in its core
132
What is the term for the coordination of many different pathways in order to regulate protein activity?
proteostasis
133
What two elements are required for a protein to be considered denatured?
the loss of its tertiary structure and accompanying loss of activity
134
How can proteins be denatured (4)?
heat/cold, pH extremes, organic solvents, chaotropic agents that break H bonds
135
Can denaturation be reversible?
yes! (but most used in lab are irreversible)
136
What is a Tm value?
the point where 50% of proteins are denatured
137
What is the significance of the 1972 Nobel Prize in Chemistry?
awarded to Christian B Anfinsen for his work concerning the connection between amino acid sequence and the functional conformation
138
Describe Christian B Anfinsen's ribonuclease refolding experiment?
- 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
What did Christian B Anfinsen conclude from his experiment?
that the amino acid sequence ALONE determines the native conformation
140
What is Levinthal's paradox?
it is mathematically impossible for protein folding occur by randomly trying ever conformation until the lowest-energy one is found
141
How can protein folding NOT be random?
direction toward the native (lowest energy) structure is always thermodynamically most favorable
142
Describe the idea of a folding funnel.
folding properties are related to free energy and the possible conformations of a protein are reduced as it approaches native-like structure
143
What is the term used to describe proteins that facilitate the folding of other proteins?
chaperonins
144
Describe the significance of the GroEL/s chaperonin?
10-15% of E. coli proteins require its hydrophobic pocket to fold
145
What is amyloidosis?
the deposition of fibrils throughout the body
146
How does the cholera toxin lead to disease?
unfolds in the ER, is transported to the cytoplasm for degradation
147
What are three disease like things caused by protein misfolding?
amyloidosis, cholera, and prions
148
What are the three principles that determine protein conformation?
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
