Protein Structure & Function Flashcards
1
Q
What structures of integral membrane proteins can pass through membranes?
A
Non-polar α-helices (can be single or multi pass)
Amphipathic secondary structures (membrane β-barrels)
2
Q
Definition
a normal cell-surface glycoprotein that is conformationally characterized by two alpha helices and two complex-type N-linked oligosaccharide chains
A
PrPc
3
Q
The bacterial flagellum…
Select one:
has the same evolutionary origin as Type IV pilus assembly
uses ATP hydrolysis as a source of energy for rotation
requires proton motive force for self-assembly but not for rotation
has a built-in Type II secretion system that exports rod, hook and filament components
uses Type III protein export for self-assembly
A
The bacterial flagellum…
Select one:
has the same evolutionary origin as Type IV pilus assembly
uses ATP hydrolysis as a source of energy for rotation
requires proton motive force for self-assembly but not for rotation
has a built-in Type II secretion system that exports rod, hook and filament components
uses Type III protein export for self-assembly
4
Q
Define
Nanodiscs
A
a synthetic model membrane system which assists in the study of membrane proteins. It is composed of a lipid bilayer of phospholipids with the hydrophobic edge screened by two amphipathic proteins.
5
Q
What are the disadvantages of protein therapeutics relative to small molecule therapeutics?
A
- Difficulty/cost of large-scale production
- Difficulty of purification
- Heterogeneity (inc. PTMs)
- Immunogenicity (if not natural human protein)
- Oral delivery not usually possible
- May degrade in plasma
- Reduced bioavailability: generally limited to extracellular targets
6
Q
How has Insulin lispro and insulin aspart been altered?
A
They are mutated so that they tend not to self-associate, whcih facilitates more rapid absorption upon administeration
7
Q
Definition
a large and complex molecular machine found primarily within the nucleus of eukaryotic cells
A
Spliceosome
8
Q
Definition
misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein
A
Prions
9
Q
Definition
a postulate in molecular biology that states that, at least for a small globular protein in its standard physiological environment, the native structure is determined only by the protein’s amino acid sequence
A
Thermodynamic hypothesis
10
Q
What are the steps in protein structure determination by NMR spectroscopy?
A
- Express the protein; enrich in stable isotopes (15N, 13C)
- Optimise sample conditions (high conc, soluble)
- Assign the 1H, 15N and 13C signals in spectra
- Collect spectra to identify pairs of atoms that are close in space
- Use distance information to calculate a family of structures
- Iterate through previous steps to refine the structural ensemble
11
Q
Define
Hit Rate
A
the number of active compounds per screen
12
Q
Define
In silico Screening
A
performed on computer or via computer simulation
13
Q
How do we know that effector proteins are unfolded when they pass through the T3SS needle?
A
The needle is a helical polymer of one protein with a diameter of 2nm, which is much smaller than most proteins so they must be unfolded when they thread through
14
Q
Define
Spliceosome
A
a large and complex molecular machine found primarily within the nucleus of eukaryotic cells
15
Q
What is QSAR used for?
A
Details of the role of various functional groups
Relative binding affinities of similar compounds
Models of pharmacophores for screening databases
16
Q
X-ray crystallography is used for determining the three-dimensional structure of proteins by
Select one:
using radiofrequency pulses that perturb the magnetically susceptible nuclei.
using X-rays that are scattered by electrons.
using X-rays that are scattered by atomic nuclei.
using electrons that bounce off the surface of molecules in an ordered array.
using radiofrequency radiation to create diffraction patterns.
A
X-ray crystallography is used for determining the three-dimensional structure of proteins by
Select one:
using radiofrequency pulses that perturb the magnetically susceptible nuclei.
using X-rays that are scattered by electrons.
using X-rays that are scattered by atomic nuclei.
using electrons that bounce off the surface of molecules in an ordered array.
using radiofrequency radiation to create diffraction patterns.
17
Q
Define
Amphipathic
A
(of a molecule, especially a protein) having both hydrophilic and hydrophobic parts.
18
Q
Define
Bioavailability
A
the proportion of a drug or other substance which enters the circulation when introduced into the body and so is able to have an active effect
19
Q
Define
Quantitative structure activity relationship (QSAR)
A
involves detailed computer modelling of the properties of a ligand or lead compound and the correlation of the information with activity data
20
Q
Define
Van de Waals interactions
A
driven by induced electrical interactions between two or more atoms or molecules that are very close to each other
21
Q
Define
Insulin glargine
A
a long-acting form of insulin used for the treatment of hyperglycemia caused by Type 1 and Type 2 Diabetes
22
Q
How is SP cryo-EM performed?
A
- Freeze the sample (vitrobot)
- Place grid into a Transmission Electron Microscopy (TEM) that has a cryostage
- Collect data
23
Q
Define
Pan-Assay Interference Compounds (PAINS)
A
chemical compounds that often give false positive results in high-throughput screens
24
Q
What is the name of the sole member of the C-chemokine family?
A
Lymphotactin
25
A high B-factor indicates what?
High mobility
26
How do people think that prion gene mutations cause disease?
The presence of prions lowers the actiation energy of the conversion of the normal protein to the prion, thus greatly increasing the probability that this conversion will happen within the average lifespac
27
In the process of engineering insulin, several strategic amino acid changes have been made to produce fast-acting or long-acting insulin. Below is a schematic showing the amino acid sequence of the two chains of insulin. Highlighted are amino acids known to interact with the insulin receptor, occur at the dimer interface or have been modified in engineered forms of insulin.
Which of the following changes could lead to a faster acting insulin without affecting receptor binding?
Select one:
A21-Asn-\> Lys
B16-Tyr -\> Arg
B19-Cys -\> Ala
B30-Thr -\> Ser
B28-Pro -\> Asp
In the process of engineering insulin, several strategic amino acid changes have been made to produce fast-acting or long-acting insulin. Below is a schematic showing the amino acid sequence of the two chains of insulin. Highlighted are amino acids known to interact with the insulin receptor, occur at the dimer interface or have been modified in engineered forms of insulin.
Which of the following changes could lead to a faster acting insulin without affecting receptor binding?
Select one:
A21-Asn-\> Lys
B16-Tyr -\> Arg
B19-Cys -\> Ala
B30-Thr -\> Ser
**B28-Pro -\> Asp**
28
How has Insulin determir been altered?
It is acylated, resulting in reversible binding to albumin and slower absorption from tissue (distributed more slowly to tissue)
29
The lower the Kd, the ______ the affinity
The lower the Kd, the **higher** the affinity
30
# Define
Glycosaminoglycans (GAGs)
long linear (unbranched) polysaccharides consisting of repeating disaccharide (double sugar) units
31
Which form of lympotactin binds to the receptor?
Monomer
32
Which of the following is NOT a step used in protein structure analysis by single particle cryo-electron microscopy?
Select one:
obtaining a monolayer of frozen protein particles
using an X-ray beam to obtain "shadow" images of the particles
superposition of many images of the particles detected at the same angle
collection of many images of single particles obtained at different angles
processing of images obtained at different angles to produce a three-dimensional model
Which of the following is NOT a step used in protein structure analysis by single particle cryo-electron microscopy?
Select one:
obtaining a monolayer of frozen protein particles
**using an X-ray beam to obtain "shadow" images of the particles**
superposition of many images of the particles detected at the same angle
collection of many images of single particles obtained at different angles
processing of images obtained at different angles to produce a three-dimensional model
33
Why are proteins frozen in different orientations for SP cryo-EM?
In order to develop a 3D image of the protein
34
Structure determination by NMR spectroscopy DOES NOT involve...
Select one:
radiofrequency pulses applied to a sample placed in a large magnetic field.
detection of radiofrequency signals derived from the electrons in the sample.
determination of which protons (1H) are close to which other protons in the sample.
calculation of three-dimensional structures that are consistent with determined distance constraints.
superimposition of three-dimensional structures calculated using the NMR data to check for consistency.
Structure determination by NMR spectroscopy DOES NOT involve...
Select one:
radiofrequency pulses applied to a sample placed in a large magnetic field.
**detection of radiofrequency signals derived from the electrons in the sample.**
determination of which protons (1H) are close to which other protons in the sample.
calculation of three-dimensional structures that are consistent with determined distance constraints.
superimposition of three-dimensional structures calculated using the NMR data to check for consistency.
35
What type of information does SAR provide?
Qualitative information
36
# Define
Hydrogen bonds
the electromagnetic attraction created between a partially positively charged hydrogen atom attached to a highly electronegative atom and another nearby electronegative atom
37
What is used to determine the position of nuclei for the PDB?
Electron density detected through diffraction
38
# Definition
a long-acting insulin analogue with a flat and predictable action profile
Insulin detemir
39
# Define
Pharmacophores
a part of a molecular structure that is responsible for a particular biological or pharmacological interaction that it undergoes
40
\_\_\_\_\_\_\_\_\_ can be used to determine the number of binding sites and the affinity of each
**Binding curves** can be used to determine the number of binding sites and the affinity of each
41
Protein-ligand interactions...
Select one:
usually occur with a Kd in the picomolar range
usually occur through the formation of covalent bonds
are usually in equilibrium between bound and unbound forms
can reach 100% bound protein as long as enough ligand is added
occur through mainly hydrophobic interactions
Protein-ligand interactions...
Select one:
usually occur with a Kd in the picomolar range
usually occur through the formation of covalent bonds
**are usually in equilibrium between bound and unbound forms**
can reach 100% bound protein as long as enough ligand is added
occur through mainly hydrophobic interactions
42
# Define
Insulin aspart
a rapid-acting form of insulin used for the treatment of hyperglycemia caused by Type 1 and Type 2 Diabetes
43
Why is NMR good for smaller molecules than for larger molecules?
The signal decays over time so in large molecules the signal is gone before it can be measured. The signal for smaller molecules lasts longer and therefore can be detected
44
What is the basic structure of T3SS?
45
What is the smallest unit of a lattice called?
Unit cell
46
# Define
Immunogenicity
the ability of a particular substance, such as an antigen or epitope, to provoke an immune response in the body of a human and other animal
47
When two chemical fragments are identified that bind adjacently in a target active site, with Kd = 100 micromolar and 2 micromolar respectively (as illustrated below), their covalent attachment would be predicted to result in a compound...
Select one:
of reduced specificity
of Kd for the target equivalent to the sum total of the fragment affinities
of improved solubility
that binds to the target with greater than an additive affinity of the fragments
that is easier to synthesise than the separate fragments
When two chemical fragments are identified that bind adjacently in a target active site, with Kd = 100 micromolar and 2 micromolar respectively (as illustrated below), their covalent attachment would be predicted to result in a compound...
Select one:
of reduced specificity
of Kd for the target equivalent to the sum total of the fragment affinities
of improved solubility
**that binds to the target with greater than an additive affinity of the fragments**
that is easier to synthesise than the separate fragments
48
Which method should be used to determine the structure of DNA and RNA?
DNA and RNA are better visualised by NMR since they don't crystalise very well
They are more "floppy" than proteins and they are charged
49
# Define
X-ray Crystallography
the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions
50
# Definition
complex bacterial structures that provide gram-negative pathogens with a unique virulence mechanism enabling them to inject bacterial effector proteins directly into the host cell cytoplasm, bypassing the extracellular milieu
Type III secretion system
51
# Define
Phase problem
the problem of loss of information concerning the phase that can occur when making a physical measurement
52
# Definition
the ability of a particular substance, such as an antigen or epitope, to provoke an immune response in the body of a human and other animal
Immunogenicity
53
# Definition
a factor that can be applied to the X-ray scattering term for each atom (or for groups of atoms) that describes the degree to which the electron density is spread out; an indication of mobility of an atom
B-factor
54
What are the three key methods used to determine protein structure?
X-ray crystallography
NMR
Electron microscopy
55
# Definition
a small cytokine belonging to the C chemokine family
Lymphotactin (Ltn)
56
What is the difference between PrPc and PrPSc?
PrPc = normal glycosylated cell-surface protein found in many tissue (particularly nerve cells). Protein is not essential
PrPSc = misfolded, prion form of PrPc
57
Why can't full injectosomes or spliceosomes be characterised using NMR or X-ray crystallography?
They are much larger than these techniques can analyse
58
What comes first?
Hits or Leads
Hits
59
True or False
The phase angle cannot be measured directly
True
60
Which has better resolution?
X-ray or NMR
X-ray
61
# Define
Docking
computational creation of a protein-ligand complex by simulation
62
What is the problem with *in silico* screening?
99% accurate scoring
In a library of 1 million compounds, 990 real actives found and 9900 false actives found
63
How has Insulin glargine been altered?
It has an increased isoelectric point which makes it less soluble at physiological pH which slows its absorption into tissue
64
Which of the following is NOT an advantage of protein therapeutics over small molecule therapeutics? Protein therapeutics...
Select one:
can have high specificity for their target.
can be immunogenic.
tend to have low toxicity.
can replace dysfunctional proteins.
can be readily engineered.
Which of the following is NOT an advantage of protein therapeutics over small molecule therapeutics? Protein therapeutics...
Select one:
can have high specificity for their target.
**can be immunogenic.**
tend to have low toxicity.
can replace dysfunctional proteins.
can be readily engineered.
65
True or False:
For X-ray crystallography to work, the structures must be arranged in a lattice
True
66
What is Docking?
Computational creation of a protein-ligand complex by simulation. Relies on a detailed structure of the protein and particularly its active site
67
Which of the following is FALSE? Single Particle cryo-Electron Microscopy can be used to determine the structure of...
Select one:
proteins or protein complexes that are membrane bound
large proteins or protein complexes to low resolution
many conformational states of a protein or protein complex
all sized proteins and peptides to low resolution
proteins or protein complexes that can not be crystallized
Which of the following is FALSE? Single Particle cryo-Electron Microscopy can be used to determine the structure of...
Select one:
proteins or protein complexes that are membrane bound
large proteins or protein complexes to low resolution
many conformational states of a protein or protein complex
**all sized proteins and peptides to low resolution**
proteins or protein complexes that can not be crystallized
68
# Definition
chemical compounds that often give false positive results in high-throughput screens
Pan-Assay Interference Compounds (PAINS)
69
What prevent polymerisation of flagellin molecules in the cytoplasm?
Chaperones
70
Which of the following chemical screening strategies will NOT increase the hit-rate in drug discovery?
Select one:
Avoiding compounds that have properties according to Lipinski’s rule of five.
Avoiding “Pan-Assay Interference” compounds that often appear as hits in assays.
The use of in silico screening of compounds to consider potential interactions with the target.
De novo design of chemical structures that have potential to fit in the active site of the target structure.
Fragment screening to identify chemical fragments that bind to the target as determined experimentally.
Which of the following chemical screening strategies will NOT increase the hit-rate in drug discovery?
Select one:
**Avoiding compounds that have properties according to Lipinski’s rule of five.**
Avoiding “Pan-Assay Interference” compounds that often appear as hits in assays.
The use of in silico screening of compounds to consider potential interactions with the target.
De novo design of chemical structures that have potential to fit in the active site of the target structure.
Fragment screening to identify chemical fragments that bind to the target as determined experimentally.
71
# Define
PrPsc
an alternatively folded variant of the cellular prion protein, PrPC, which is a regular, GPI-anchored protein that is present on the cell surface of neurons and other cell types
72
# Definition
involves detailed computer modelling of the properties of a ligand or lead compound and the correlation of the information with activity data
Quantitative structure activity relationship (QSAR)
73
# Definition
the stationary part of a rotary system, found in electric generators, electric motors, sirens, mud motors or biological rotors
Stator ring
74
The B-factor is only meaningful in structures determined how?
Using X-ray diffraction
75
Why is one considered strong while the other is weak?
The electron orbitals of the oxygen overlap with the hydrogen for the strong one
76
# Definition
driven by induced electrical interactions between two or more atoms or molecules that are very close to each other
Van de Waals interactions
77
How does the absorption rate of insulin change as the number of subunits (i.e. monomer, dimer) increases?
Monomor absorbs fastest
Monomer \> Dimer \> Tetramer \> Zn-Hexamer
78
For most proteins, alternative native conformations exist in dynamic equilibrium, what is the exception?
Prions
79
# Define
Nuclear magnetic resonance (NMR)
a physical observation in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field and therefore not involving electromagnetic waves) and respond by producing an electromagnetic signal with a frequency characteristic of the magnetic field at the nucleus
80
True or False:
Protein structures are fixed
False
Protein structures are dynamic
81
# Definition
a protein structure found at the base of a eukaryotic undulipodium (cilium or flagellum)
Basal body
82
What does QSAR involve?
Detailed computer modelling of the properties of a ligand or lead compound and the correlation of this information with activity data (no knowledge of target required)
83
What type of amino acids does a multi pass α-helix have?
Amphipathic
i.e. having both hydrophillic and hydrophobic regions
84
The NMR signal is derived from what?
The radiofrequency signals of magnetically susceptible nuclei
85
# Define
Prions
misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein
86
What are the problems with drug design?
* Biological systems are notoriously finicky
* Protein movements
* Adaptation to ligand
* Weak bonds very important
* One H bond = ~10x ligand affinity
* Non-standard bonds
* CH H bond donors, CF 'fluorine' bonds
* Little mistakes in the structures = big mistakes in the models
87
Why is the (O=)C-N bond considered partially double?
Resonance. This prevents rotation around this bond making it planar
88
Which protein structure level does PrPc and PrPSc differ?
Secondary
Tertiary
(Quaternary)
89
What is the mathematical relationship between the fraction of P bound and the free concentration of L?
Fraction P bound = [L]/(Kd + [L])
Rearrange the dissociation constant equation
90
What is the proton motive force used for in the flagellum?
Energises the translocation of unfolded proteins through the channel in the flagellum during its self-assembly
Produces the ernergy for the rotation of flagellum
91
# Define
Attrition
when participants leave during a study
92
The low resolution SP-cryo EM structure of the perforin pore shows that it is large enough for granzyme B to be...
Select one:
passively translocated in an unfolded state
actively translocated in an unfolded state
passively translocated in a folded state
actively translocated in a folded state
blocked from passing through the pore
The low resolution SP-cryo EM structure of the perforin pore shows that it is large enough for granzyme B to be...
Select one:
passively translocated in an unfolded state
actively translocated in an unfolded state
**passively translocated in a folded state**
actively translocated in a folded state
blocked from passing through the pore
93
What are the fast-acting insulin analogues?
Insulin lispro
Insulin aspart
94
# Definition
the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions
X-ray Crystallography
95
# Definition
antibodies from non-human species whose protein sequences have been modified to increase their similarity to antibody variants produced naturally in humans
Humanised therapeutic antibodies
96
What are the steps in protein structure determination by X-ray crystallography?
1. Express/purify the protein
2. Crystallise the protein (can't be dry)
3. Collect diffraction data
4. Determine the space group, unit cell dimensions, and number/symmetry of molecules per unit cell
5. Solve the "phase problem" (phase angle)
6. Calculate an electron density map
7. Build a molecular model to fit the electron density map
8. Refine the model
97
# Define
Basal body
a protein structure found at the base of a eukaryotic undulipodium (cilium or flagellum)
98
# Definition
long linear (unbranched) polysaccharides consisting of repeating disaccharide (double sugar) units
Glycosaminoglycans (GAGs)
99
Why does the species barrier exist for prions?
The species barrier exists because a certain degrees of sequence identity/similarity between the host PrPc and the acquired PrPSc is required for the interaction and catalysis to occur
100
What techniques can we use if we have known ligands but no known target structure?
QSAR
Scaffold hopping
101
The basal body of the bacterial flagellum and bacterial injectisome is used to secrete monomers that, once outside of the cell, polymerise into the filament and needle, respectively. What prevents them from polymerisation inside the cell?
Select one:
Protein chain is fed into the secretion channel as it is being synthesized
They need metal ion for polymerisation, which is only available outside
They are held in an unfolded state by intracellular chaperones
They require energy of ATP hydrolysis to polymerise
They require proton-motive force to polymerise
The basal body of the bacterial flagellum and bacterial injectisome is used to secrete monomers that, once outside of the cell, polymerise into the filament and needle, respectively. What prevents them from polymerisation inside the cell?
Select one:
Protein chain is fed into the secretion channel as it is being synthesized
They need metal ion for polymerisation, which is only available outside
**They are held in an unfolded state by intracellular chaperones**
They require energy of ATP hydrolysis to polymerise
They require proton-motive force to polymerise
102
# Definition
tendency of nonpolar substances to aggregate in an aqueous solution and exclude water molecules
Hydrophobic interactions
103
Why is hydrogen atoms not displayed in X-ray crystallography?
Hydrogens can't be seen because 1 electrion is often not enough to produce a signal
104
Which method currently contributes the most to the PDB database?
X-ray crystallography
105
# Define
Monoclonal antibodies
antibodies that are made by identical immune cells that are all clones of a unique parent cell.
106
Integral membrane proteins use *polar/non-polar* amino acids to interact with the lipid membrane
Integral membrane proteins use **non-polar** amino acids to interact with the lipid membrane
107
How is the secretion apparatus of the flagellum used?
The basal body of the flagellar motor functions as a T3SS that is used to secrete proteins that will polymerise into the hook and the filament of the flagellum. So the secretion apparatus of the flagellum is used only for its self-assembly
108
# Definition
when participants leave during a study
Attrition
109
How do we improve the results of high-throughput screening?
* Lipinski rule of 5
* Remove "Promiscuous" inhibitors
110
Why are protein structures intrinsically dynamic?
There are many possible conformations since rotation can occur easily around single bonds
111
What does 2D H NMR tell you that 1D can't?
Indicates proteins that are correlated i.e. within 5Å of each other
112
How does the proton motive force (PMF) work?
Food substrates (such as lactose) are delivered to the cytoplasm. Catabolic enzymes extract energy from these substrates in the form of electrons, which are delivered to the cell membrane by the hydrogen carrier, NAD.
These electrons flow via the electron transport chain. This electron flow is used to drive proton flow to the periplasmic spae. As the protons accumulate in the periplasm, the difference in concentration of protons in the periplasm and cytoplasm gives rise to the PMF that is used to drive ATP synthesis, flagellar motility and membrane transport
113
# Define
Multidimensional heteronuclear NMR
a type of NMR where protein can be prepared with isotopic labels and then 2D and 3D NMR experiments conducted which allows through-bond connections and NOES to be visualise and measured
114
# Definition
the transfer of energy by radio waves
Radiofrequency pulse (rf)
115
# Definition
compounds whose inhibition mechanism involves the interaction of aggregates of many compound molecules with the target protein, rather than the binding of individual molecules
Promiscuous inhibitors
116
Which statement applies to prions but not viruses?
Select one:
They are infectious agents that are not cells
They rely on a host cell to provide the machinery for their replication
Their propagation does not rely on the replication of genetic information
The diseases they cause may be fatal
They can only be contracted from an infected source
Which statement applies to prions but not viruses?
Select one:
They are infectious agents that are not cells
They rely on a host cell to provide the machinery for their replication
**Their propagation does not rely on the replication of genetic information**
The diseases they cause may be fatal
They can only be contracted from an infected source
117
What are some examples of protein engineering to improve therapeutic utility?
* Insulin
* Enhancement of bioavailable profile
* Monoclonal antibodies
* Reduction of immunogenicity
118
A decrease in the resolution of a PDB structure indicates what?
Increased accuracy
119
Why can X-rays be used to determine protein structure?
In order to see the molecules it is necessary to use a form of electromagnetic radiation with a wavelength on the order of bond lengths, such as X-rays
120
What is the basic principle of NMR?
While the sample is in a very string magnetic field, the nuclei resonate at specific radiofrequencies. After a short radiofrequency pulse that perturbs the energy levels of the system, the nuclei emit theur own individual radiofrequency signals that can be detected
121
What is Docking used for?
Derive theoretical structures of unsolved complexes
Investigate details of ligand-protein interaction
122
What are the limits to SP cryo-EM resolution?
Images- number and quality of particles
Expensive equipment
Experitise needed
Orientation bias
Heterogeneity of sample
123
Does the hydrophobic section of a multi pass α-helix tolerate polar residues? Why are they there?
No
124
What is SP cryo-EM used for?
Used to understand the structure of large molecular protein assemblies and integral membrane proteins
125
What does QSAR give us?
Accurate hit development
126
What is different about the C-chemokine family?
It is missing the first of two disulphide bonds
127
What is the cause of hydrophobic interactions?
The system wants to achieve the greatest thermodynamic stability by minimising the number of ordered water molecules required to surround hydrophobic portions of the solute molecules
128
# Definition
an important tool to identify stereochemistry of proteins and other biomolecules in solution, whereas in solid form crystal x-ray diffraction must be used to identify the stereochemistry
2D NOESY
129
Why are prions difficult to detect using conventional methods?
There are no gene, so no PCR
Antibodies to them are not produced, so no serology
Brain tissue is not easily accessible
130
# Define
Insulin lispro
a short-acting, manmade version of human insulin
131
# Definition
a peptide hormone produced by beta cells of the pancreatic islets
Insulin
132
# Define
Leads
a chemical compound that has pharmacological or biological activity likely to be therapeutically useful, but may nevertheless have suboptimal structure that requires modification to fit better to the target
133
# Define
PrPc
a normal cell-surface glycoprotein that is conformationally characterized by two alpha helices and two complex-type N-linked oligosaccharide chains
134
How can Promiscuous inhibitors be identified?
Detergent removes their binding ability
135
What is SP cryo-EM good for?
* Put in information about nanodiscs, liposomes and detergents
* Integral membrane proteins
* Solubilised in detergent
* Embedded in nanodiscs
* Embedded in liposomes
* Proteins with different conformations/assembly states
* Things that do not crystallise!
136
# Definition
a short-acting, manmade version of human insulin
Insulin lispro
137
What techniques can we use if we know the target structure but not known ligands?
* In silico* screening
* De novo* design
138
# Definition
the proportion of a drug or other substance which enters the circulation when introduced into the body and so is able to have an active effect
Bioavailability
139
# Define
Heteronuclear single quantum coherence (HSQC)
used frequently in NMR spectroscopy of organic molecules and is of particular significance in the field of protein NMR
140
What is SP cryo-EM not good for?
* Membrane proteins embedded in cells
* Very small proteins
* Disordered proteins
141
How do we improve hit rate?
*in silico* screening
142
How does a T3SS work?
Translocator proteins are delivered through a needle and form the pore
Effector proteins are injected into the target cell
Effector proteins are unfolded in the cytoplasm and threaded into the needle complex
T3S chaperines mediate unfolding of the effector proteins prior to export
ATPase is required for chaperone mediated unfolding
143
# Definition
a chemical compound that has pharmacological or biological activity likely to be therapeutically useful, but may nevertheless have suboptimal structure that requires modification to fit better to the target
Leads
144
# Definition
the number of active compounds per screen
Hit Rate
145
# Definition
a physical observation in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field and therefore not involving electromagnetic waves) and respond by producing an electromagnetic signal with a frequency characteristic of the magnetic field at the nucleus
Nuclear magnetic resonance (NMR)
146
# Definition
the net result of the attractive forces between the positively charged nuclei and the negatively charged electrons of the two molecules
Electrostatic interactions
147
What does each of these methods provide?
X-ray, NMR
X-ray results in a single structure
NMR results in an ensemble of structures
148
What are pharmacophores?
Map of the physicochemical properties that give your compound activity
149
# Define
Structure-activity relationship (SAR)
the relationship between the chemical structure of a molecule and its biological activity
150
# Define
Lymphotactin (Ltn)
a small cytokine belonging to the C chemokine family
151
# Definition
the force that promotes movement of protons across membranes downhill the electrochemical potential
Proton motive force
152
# Define
Hydrophobic interactions
tendency of nonpolar substances to aggregate in an aqueous solution and exclude water molecules
153
What are the properties of the amino acids in transmembrane β-barrels?
Amphipathetic β-strands alternate non-polar with polar
154
What does *In silico* screening and *De novo* design give us?
New hits
155
# Definition
performed on computer or via computer simulation
In silico Screening
156
The "resolution" of a protein X-ray crystallography structure...
Select one:
refers to how well defined the position of the atoms are in the crystal structure.
is dependent upon the size of the crystal.
refers to the molecular motion of each atom.
is dependent upon the solvent content of the crystal.
refers to how many molecules exist in each unit cell.
The "resolution" of a protein X-ray crystallography structure...
Select one:
**refers to how well defined the position of the atoms are in the crystal structure.**
is dependent upon the size of the crystal.
refers to the molecular motion of each atom.
is dependent upon the solvent content of the crystal.
refers to how many molecules exist in each unit cell.
157
# Definition
used frequently in NMR spectroscopy of organic molecules and is of particular significance in the field of protein NMR
Heteronuclear single quantum coherence (HSQC)
158
# Define
Hits
the right small molecules which bind to the target and modify its function
159
A _______ angle for each X-ray reflection are required to determine a crystal structure
A **phase** angle for each X-ray reflection are required to determine a crystal structure
160
# Definition
computational creation of a protein-ligand complex by simulation
Docking
161
# Definition
an alternatively folded variant of the cellular prion protein, PrPC, which is a regular, GPI-anchored protein that is present on the cell surface of neurons and other cell types
PrPsc
162
Which of the two ligands has a higher affinity to protein?
Red
163
True or False
Proteins must be crystallised for NMR to determine structure
False
The protein should be in solution
164
The killing of tumour cells using _____________ can result from receptor blockade, payload delivery or other mechanisms
The killing of tumour cells using **monoclonal antibodies (mAbs)** can result from receptor blockade, payload delivery or other mechanisms
165
Why of intrinsic defense mechanisms not exist for prions?
They are host's own proteins
They are not poisonous
166
What is the usually hit rate? What about the rate of useful activity?
Usual: 0.1%
Useful: 0.01%
167
# Definition
the problem of loss of information concerning the phase that can occur when making a physical measurement
Phase problem
168
# Define
Nanomachines
a mechanical or electromechanical device whose dimensions are measured in nanometers (millionths of a millimeter, or units of 10 -9 meter)
169
# Definition
(of a molecule, especially a protein) having both hydrophilic and hydrophobic parts.
Amphipathic
170
# Definition
a graph that can be used to determine the number of binding sites and the affinity of each protein
Binding curves
171
# Definition
the relationship between the chemical structure of a molecule and its biological activity
Structure-activity relationship (SAR)
172
Below is a two-dimensional 1H NMR NOESY spectrum acquired for a protein. What do the crosspeaks (the signals that are not on the diagonal of the spectrum) represent?
## Footnote
These are signals that indicate that...
Select one:
a particular 1H is bonded to another particular 1H.
a ligand is bound to the protein.
one 1H is in two different electronic environments.
a particular 1H is close to other particular 1H through space.
the sample is also labelled with 15N.
Below is a two-dimensional 1H NMR NOESY spectrum acquired for a protein. What do the crosspeaks (the signals that are not on the diagonal of the spectrum) represent?These are signals that indicate that...
Select one:
a particular 1H is bonded to another particular 1H.
a ligand is bound to the protein.
one 1H is in two different electronic environments.
**a particular 1H is close to other particular 1H through space.**
the sample is also labelled with 15N.
173
In protein X-ray crystallography, the protein must exist in crystalline form because...
Select one:
this reduces the water content of the sample.
having the molecules in an ordered array reduces molecular flexibility.
the electron clouds around the atoms become better resolved.
having many molecules in an ordered array results in a diffraction pattern being produced from an X-ray beam.
this allows the sample to be picked up and placed in front of the X-ray beam.
In protein X-ray crystallography, the protein must exist in crystalline form because...
Select one:
this reduces the water content of the sample.
having the molecules in an ordered array reduces molecular flexibility.
the electron clouds around the atoms become better resolved.
**having many molecules in an ordered array results in a diffraction pattern being produced from an X-ray beam.**
this allows the sample to be picked up and placed in front of the X-ray beam.
174
What is the energy of ATP hydolysis used for in T3SS and flagella?
**T3SS:** to unfold the effector proteins
**Flagellum:** to unfold the components of the rod, hook and filament
175
# Definition
a rule of thumb to evaluate druglikeness or determine if a chemical compound with a certain pharmacological or biological activity has chemical properties and physical properties that would make it a likely orally active drug in humans
Lipinski Rule of Five
176
True or False:
Prion infection is 100% fatal
True
177
The NMR structure reveals regions of protein \_\_\_\_\_\_\_\_
The NMR structure reveals regions of protein **flexibility**
178
What are the steps of *in silico* screening?
1. Take the structure of a target biomolecule
2. Take a library of commercially available small molecule structures
3. Fit every small molecule into the protein target, scoring how well it fits
4. Rank the scored small molecules
5. Buy a selection of the top of the ranked list and test in your *in vitro* assay
179
How is prion disease usually confirmed?
Postmortem histopathology test of brain tissue
180
# Define
Insulin
a peptide hormone produced by beta cells of the pancreatic islets
181
# Definition
a mechanical or electromechanical device whose dimensions are measured in nanometers (millionths of a millimeter, or units of 10 -9 meter)
Nanomachines
182
# Define
Radiofrequency pulse (rf)
the transfer of energy by radio waves
183
What does the dimer form of lymphotactin do?
Binds to glycosaminoglycans (GAGs) with high affinity, adhering to the surface of vascular endothelial cells
184
How is a sample prepared for SP cryo-EM?
Pure, low-concentration sample
185
Nuclear magnetic resonance (NMR) study showed that lymphotactin (Ltn) adopts two distinct structures in equilibrium. Which of the following statements is correct?
Select one:
The two folds have the same secondary structure but different oligomeric states
The monomeric and dimeric forms have high affinity to the lymphotactin receptor and glucosaminoglycans, respectively
The two structures have different posttranslational modifications
The two structures arise because of a different length of the polypeptide chain
The two folds have the same oligomeric state but different secondary structure
Nuclear magnetic resonance (NMR) study showed that lymphotactin (Ltn) adopts two distinct structures in equilibrium. Which of the following statements is correct?
Select one:
The two folds have the same secondary structure but different oligomeric states
**The monomeric and dimeric forms have high affinity to the lymphotactin receptor and glucosaminoglycans, respectively**
The two structures have different posttranslational modifications
The two structures arise because of a different length of the polypeptide chain
The two folds have the same oligomeric state but different secondary structure
186
# Define
Proton motive force
the force that promotes movement of protons across membranes downhill the electrochemical potential
187
Consider the small ligand molecule bound in a pocket in a protein shown below, and identify the binding interactions that are labelled i-iv.
## Footnote
The interaction labelled iv is:
Select one:
a salt bridge
a covalent bond
a hydrogen bond
a van der Waals contact
hydrophobic
Consider the small ligand molecule bound in a pocket in a protein shown below, and identify the binding interactions that are labelled i-iv.
## Footnote
The interaction labelled iv is:
Select one:
**a salt bridge**
a covalent bond
a hydrogen bond
a van der Waals contact
hydrophobic
188
What is the proton motive force used for in the T3SS?
The actual translocation of effector proteins through the needle
189
What non-covalent interactions are involved in protein folding?
Van der Waals interactions
Hydrogen bonds
Electrostatic interactions
Hydrophobic interactions
190
# Define
Lipinski Rule of Five
a rule of thumb to evaluate druglikeness or determine if a chemical compound with a certain pharmacological or biological activity has chemical properties and physical properties that would make it a likely orally active drug in humans
191
# Definition
antibodies that are made by identical immune cells that are all clones of a unique parent cell.
Monoclonal antibodies
192
# Define
Electrostatic interactions
the net result of the attractive forces between the positively charged nuclei and the negatively charged electrons of the two molecules
193
Which came first?
T3SS or flagella
T3SS evolved from bacterial flagellum
194
The 20 Angstroms diameter of the hollow channel inside the injectisome’s needle suggests that...
Select one:
it can only secrete small molecules – e.g. sugars
it can only secrete small proteins
secretion does not involve passage through the needle
proteins travel through it in unfolded form
it is large enough to secrete any protein
The 20 Angstroms diameter of the hollow channel inside the injectisome’s needle suggests that...
Select one:
it can only secrete small molecules – e.g. sugars
it can only secrete small proteins
secretion does not involve passage through the needle
**proteins travel through it in unfolded form**
it is large enough to secrete any protein
195
Upon accessing a PDBID, a large amount of information is available. What are the two key things?
1. The three-dimensional x, y, z coordinates of all the atoms in a macromolecular structure
2. The data used to determine the structure
196
# Definition
the electromagnetic attraction created between a partially positively charged hydrogen atom attached to a highly electronegative atom and another nearby electronegative atom
Hydrogen bonds
197
What information can NMR provide other than protein structure?
Binding sites, dynamics, equillibrium, kinetics, chemical processes
198
Using the following equation, what fraction of P is bound when [L] = 10 nM and Kd = 1 nM?
Fraction P bound = [L]/(Kd+[L])
0.9
199
200
# Define
Equilibrium dissociation constant
measures the propensity of a larger object to separate (dissociate) reversibly into smaller components, as when a complex falls apart into its component molecules
201
# Define
Stator ring
the stationary part of a rotary system, found in electric generators, electric motors, sirens, mud motors or biological rotors
202
What is the formula for the equilibrium dissociation constant?
Kd = [P][L]/[PL]
203
# Definition
measures the propensity of a larger object to separate (dissociate) reversibly into smaller components, as when a complex falls apart into its component molecules
Equilibrium dissociation constant
204
# Definition
a rapid-acting form of insulin used for the treatment of hyperglycemia caused by Type 1 and Type 2 Diabetes
Insulin aspart
205
Why is the C-ring of flagella thicker than T3SS?
The C-ring of flagella is thicker due to the stator ring that generates force. Since T3SS doesn't require movement, it doesn't have a stator ring
206
Prions are proteins that...
Select one:
are famous in that they are predisposed to form knots
cause immune response-mediated inflammation of the brain (Kuru)
can adopt two different native conformations, one of which irreversibly aggregates
are safe to eat if cooked or pickled in vinegar (acetic acid)
highly infections particles that readily pass species barrier
Prions are proteins that...
Select one:
are famous in that they are predisposed to form knots
cause immune response-mediated inflammation of the brain (Kuru)
**can adopt two different native conformations, one of which irreversibly aggregates**
are safe to eat if cooked or pickled in vinegar (acetic acid)
highly infections particles that readily pass species barrier
207
What are the advantages of protein therapeutics relative to small molecule therapeutics?
* High specificty and hence a reduced side-effect profile
* Low toxicity
* Can replace deficient or dysfunctional natural proteins
* Faster development and approval times (by ~1 year)
* Patent protection relatively straightforward
* Proteins can be readily engineered to improve properties
208
What are the Lipinski Rule of 5 criteria?
MW \< 500
logP \< 5
Hbond donors \<= 5
Hbond acceptors \<=10
209
# Definition
a part of a molecular structure that is responsible for a particular biological or pharmacological interaction that it undergoes
Pharmacophores
210
Protein structural data can be stored in and retrieved from ___ files
Protein structural data can be stored in and retrieved from **PDB** files
211
Which type of NMR are used to study protein?
1H
13C
15N
212
NMR spectroscopy cannot be used for the determination of very large structures (\> 100 kDa) because...
Select one:
very large proteins can not be prepared at high concentration.
very large proteins tumble too fast for the radiofrequency signals to be detected.
very large proteins might not crystallise.
very large proteins can not be prepared with isotopic labels.
the radiofrequency signals do not last long enough to be measured in the case of larger, slow tumbling proteins.
NMR spectroscopy cannot be used for the determination of very large structures (\> 100 kDa) because...
Select one:
very large proteins can not be prepared at high concentration.
very large proteins tumble too fast for the radiofrequency signals to be detected.
very large proteins might not crystallise.
very large proteins can not be prepared with isotopic labels.
**the radiofrequency signals do not last long enough to be measured in the case of larger, slow tumbling proteins.**
213
# Define
Binding curves
a graph that can be used to determine the number of binding sites and the affinity of each protein
214
Which metal ion stabilises the hexamer form of insulin?
Zn
215
# Definition
a long-acting form of insulin used for the treatment of hyperglycemia caused by Type 1 and Type 2 Diabetes
Insulin glargine
216
# Define
B-factor
a factor that can be applied to the X-ray scattering term for each atom (or for groups of atoms) that describes the degree to which the electron density is spread out; an indication of mobility of an atom
217
When does Van der Waals interactions occur?
They occur between electrically neutral groups in close contact due to a combination of short-range attractive forces and short-range repulsive forces due to imbalance in electron distribution
218
What technique do we use if we have no known ligand and no target structure?
High throughput screening (HTS)
219
# Define
Insulin detemir
a long-acting insulin analogue with a flat and predictable action profile
220
# Definition
the right small molecules which bind to the target and modify its function
Hits
221
Why are logarithmic scales sometimes used as binding curves?
It makes the maximum more obvious
222
Which has faster data collection?
X-ray or NMR
X-ray
223
What is the name of the chemokine that breaks the "one sequence, one fold" paradigm?
Lymphotactin (Ltn)
224
# Define
Thermodynamic hypothesis
a postulate in molecular biology that states that, at least for a small globular protein in its standard physiological environment, the native structure is determined only by the protein's amino acid sequence
225
# Define
Promiscuous inhibitors
compounds whose inhibition mechanism involves the interaction of aggregates of many compound molecules with the target protein, rather than the binding of individual molecules
226
The 100% humanization of therapeutic antibodies can be achieved...
Select one:
by grafting the variable region from the mouse monoclonal antibody onto a human monoclonal antibody.
by grafting CDR loops from the mouse monoclonal antibody onto a human monoclonal antibody.
only by using a mouse that has a ‘humanised’ set of immunolglobulin (IgG) genes for raising antibodies.
only by using a phage display system that displays a library of human antibodies.
by either using a mouse that has a ‘humanised’ set of immunolglobulin (IgG) genes or a phage display system that displays a library of human antibodies.
The 100% humanization of therapeutic antibodies can be achieved...
Select one:
by grafting the variable region from the mouse monoclonal antibody onto a human monoclonal antibody.
by grafting CDR loops from the mouse monoclonal antibody onto a human monoclonal antibody.
only by using a mouse that has a ‘humanised’ set of immunolglobulin (IgG) genes for raising antibodies.
only by using a phage display system that displays a library of human antibodies.
**by either using a mouse that has a ‘humanised’ set of immunolglobulin (IgG) genes or a phage display system that displays a library of human antibodies.**
227
Kd of *Heliobacter pylori* chemoreceptor TipC to its natural ligands lactate is 0.1 mM. Is this strong or weak binding?
Weak
228
What does Scaffold hopping give us?
Altered hit series
229
# Define
Type III secretion system
complex bacterial structures that provide gram-negative pathogens with a unique virulence mechanism enabling them to inject bacterial effector proteins directly into the host cell cytoplasm, bypassing the extracellular milieu
230
Does the hydrophilic section of a multi pass α-helix tolerate non-polar residues? Why are they there?
Yes, non-polar residues interact with other non-polar residues when located in the hydrophilic section
231
If a protein-ligand interaction is determined to have a Kd = 1 nM, and the concentration of the protein is very much less than 1 nM, the what is the approximate fraction of bound protein when the ligand concentration is 10 nM?
Select one:
0. 999
0. 99
0. 9
0. 1
0. 01
If a protein-ligand interaction is determined to have a Kd = 1 nM, and the concentration of the protein is very much less than 1 nM, the what is the approximate fraction of bound protein when the ligand concentration is 10 nM?
Select one:
0. 999
0. 99
**0.9**
0. 1
0. 01
232
Which part of a protein usually has the highest B-factor? What about the lowest?
Atoms that are on the surface are usually the most mobile. Atoms that are buried in the core of the protein are usually hardly moving at all. The hydrophobic core often has the lowest B-factor
233
Why is caution required if the part of the molecule you are interested in has high B-factors?
This will mean that the position of these atoms is not well determined
234
What type of amino acids does a single pass α-helix have?
Non-polar
235
For which of the following drug discovery methodologies is the three-dimensional structure of the protein target required? (choose the best answer)
Select one:
Fragment screening for the purpose of joining adjacent fragments together
In silico docking
Quantitative structure activity relationship (QSAR) analysis
All of fragment screening, in silico docking and quantitative structure activity relationship (QSAR) analysis.
Fragment screening and in silico docking
For which of the following drug discovery methodologies is the three-dimensional structure of the protein target required? (choose the best answer)
Select one:
Fragment screening for the purpose of joining adjacent fragments together
In silico docking
Quantitative structure activity relationship (QSAR) analysis
All of fragment screening, in silico docking and quantitative structure activity relationship (QSAR) analysis.
**Fragment screening and in silico docking**
236
# Define
Humanised therapeutic antibodies
antibodies from non-human species whose protein sequences have been modified to increase their similarity to antibody variants produced naturally in humans
237
# Definition
a synthetic model membrane system which assists in the study of membrane proteins. It is composed of a lipid bilayer of phospholipids with the hydrophobic edge screened by two amphipathic proteins.
Nanodiscs
238
True or False:
SP cryo-EM cannot be used to look at proteins in different conformational states
False
SP cryo-EM _can_ be used to look at proteins in different conformational states
239
# Define
2D NOESY
an important tool to identify stereochemistry of proteins and other biomolecules in solution, whereas in solid form crystal x-ray diffraction must be used to identify the stereochemistry
240
What are the long-acting insulin analogues?
Insulin glargine
Insulin determir
241
# Define
Injectisome
A needle-like projection of protein, in some bacteria, used as a sensory probe
242
Why are crystals needed for X-ray crystallography?
The electrons within a single molecule will scatter X-rays, however we are unable to measure the scattering
A crystal which contains a repeating pattern of molecules essentially provides a way of amplifying the signel of the scattered X-rays
243
What do you use when you have a lead series of active compounds but they suck?
Scaffold hopping
244
# Definition
A needle-like projection of protein, in some bacteria, used as a sensory probe
Injectisome
245
When is the relationship of Kd and concentrations to the proportion bound valid?
Valid only is [P] \<\< Kd
246
Protein structures can be determined by analysing ______ diffraction from single crystals
Protein structures can be determined by analysing **X-ray** diffraction from single crystals
247
How is the T3SS and flagellum similar?
The structures of the basal bodies are very similar, and both have a C-ring at the cytoplasmic side which serves as a docking platform for ATPase
They both have a helical tubular structure (flagella and needle) that is a polymer of one protein that grow from the tip
248
# Definition
a type of NMR where protein can be prepared with isotopic labels and then 2D and 3D NMR experiments conducted which allows through-bond connections and NOES to be visualise and measured
Multidimensional heteronuclear NMR
249
NMR spectroscopy cannot be used for the determination of large protein structures because...
Select one:
large protein cannot be prepared with isotopic labels
large proteins tumble too quickly in solution
large proteins cannot be purified easily
the signals from large proteins decay too quickly to be detected
NMR spectroscopy cannot be used for the determination of large protein structures because...
Select one:
large protein cannot be prepared with isotopic labels
large proteins tumble too quickly in solution
large proteins cannot be purified easily
**the signals from large proteins decay too quickly to be detected**
250
Van der Waals interactions...
Select one:
are short-range attraction/repulsion forces
occur only between oppositely charged atoms
are described by the Coulomb’s law
occur only between apolar side chains
Van der Waals interactions...
Select one:
**are short-range attraction/repulsion forces**
occur only between oppositely charged atoms
are described by the Coulomb’s law
occur only between apolar side chains
251
Chemokine lymphotactin can adopt two different native conformations that...
Select one:
have different functions
cannot coexist in solution
have the same secondary structure
inactivate the lymphotactin receptor
Chemokine lymphotactin can adopt two different native conformations that...
Select one:
**have different functions**
cannot coexist in solution
have the same secondary structure
inactivate the lymphotactin receptor
252
NMR spectroscopy can be used to determine the structures of small proteins. This method involves...
Select one:
detecting radioactivity emitted by atomic nuclei in the protein
measuring diffraction spots formed from radioisotope
detecting radiofrequency signals emitted by atomic nuclei in the protein
preparing radioactive protein samples
NMR spectroscopy can be used to determine the structures of small proteins. This method involves...
Select one:
detecting radioactivity emitted by atomic nuclei in the protein
measuring diffraction spots formed from radioisotope
**detecting radiofrequency signals emitted by atomic nuclei in the protein**
preparing radioactive protein samples
253
In the transmission of prion diseases, the infective agent is...
Select one:
a virus
a protein
DNA
RNA
In the transmission of prion diseases, the infective agent is...
Select one:
a virus
**a protein**
DNA
RNA
254
If a 1:1 protein-ligand interaction is characterised by a dissociation constant (Kd) = 1 nM, and the concentration of the protein is very much less than 1 nM, what is the approximate fraction of bound protein when the ligand concentration is 1 nM?
Select one:
1. 0
0. 5
0. 99
0. 1
If a 1:1 protein-ligand interaction is characterised by a dissociation constant (Kd) = 1 nM, and the concentration of the protein is very much less than 1 nM, what is the approximate fraction of bound protein when the ligand concentration is 1 nM?
Select one:
1.0
**0.5**
0. 99
0. 1
255
Below is a 1H-15N HSQC spectrum acquired for an 15N-labelled protein. There is one signal for every NH group in the protein.
What do the contoured spots represent?
Select one:
signals from each and every 1H nucleus in the protein
signals from 1H and 15N nuclei that are covalently bonded to each other
signals from 1H and 15N nuclei that are close to each other through space
signals that arise due to ligand binding
What do the contoured spots represent?
Select one:
signals from each and every 1H nucleus in the protein
**signals from 1H and 15N nuclei that are covalently bonded to each other**
signals from 1H and 15N nuclei that are close to each other through space
signals that arise due to ligand binding
256
Below is the amino acid sequence of the region of an integral membrane protein that spans the membrane. Have a close look at the sequence and identify the amino acids that have non-polar side chains.
## Footnote
634EGCPTNGPKQPSIAVGIVGALLLLLVVALGIGLFIRRRHTNRKR677
Note the 20 amino acid structures shown below.
What kind of secondary structure is used to span the membrane?
Select one:
amphipathic β-strand
amphipathic α-helix
hydrophilic β-strand
nonpolar α-helix
What kind of secondary structure is used to span the membrane?
Select one:
amphipathic β-strand
amphipathic α-helix
hydrophilic β-strand
**nonpolar α-helix**
257
Below is the amino acid sequence of the region of an integral membrane protein that spans the membrane. Have a close look at the sequence and identify the amino acids that have non-polar side chains.
## Footnote
634EGCPTNGPKQPSIAVGIVGALLLLLVVALGIGLFIRRRHTNRKR677
Note the 20 amino acid structures shown below.
How many times does this protein sequence span the membrane?
Select one:
once
twice
three times
four times
How many times does this protein sequence span the membrane?
Select one:
**once**
twice
three times
four times
258
Below is the amino acid sequence of the region of an integral membrane protein that spans the membrane. Have a close look at the sequence and identify the amino acids that have non-polar side chains.
634EGCPTNGPKQPSIAVGIVGALLLLLVVALGIGLFIRRRHTNRKR677
Note the 20 amino acid structures shown below.
Look at the amino acid residue F667 and consider what would happen if it was substituted with a different residue. Which amino acid residue at this position is likely to be the least disruptive to the structure of this protein?
Select one:
aspartic acid
arginine
lysine
leucine
Look at the amino acid residue F667 and consider what would happen if it was substituted with a different residue. Which amino acid residue at this position is likely to be the least disruptive to the structure of this protein?
Select one:
aspartic acid
arginine
lysine
**leucine**
259
X-ray crystallography is the most successful technique for determining the three-dimensional structure of biological macromolecules. To publish a scientific journal article describing the crystal structure it is generally a requirement that the structure is submitted to the Protein DataBank. All structures in the Protein DataBank are publicly available.
One can make a cartoon representation of protein crystal structure that is coloured by the B-factor. What does the B-factor describe?
Select one:
The thermal motion or disorder of the protein along its chain
The location of surface epitopes
The resolution of the structure
The position of amino acid sidechains relative to mainchain atoms
X-ray crystallography is the most successful technique for determining the three-dimensional structure of biological macromolecules. To publish a scientific journal article describing the crystal structure it is generally a requirement that the structure is submitted to the Protein DataBank. All structures in the Protein DataBank are publicly available.
One can make a cartoon representation of protein crystal structure that is coloured by the B-factor. What does the B-factor describe?
Select one:
**The thermal motion or disorder of the protein along its chain**
The location of surface epitopes
The resolution of the structure
The position of amino acid sidechains relative to mainchain atoms
260
X-ray crystallography is the most successful technique for determining the three-dimensional structure of biological macromolecules. To publish a scientific journal article describing the crystal structure it is generally a requirement that the structure is submitted to the Protein DataBank. All structures in the Protein DataBank are publicly available.
What parameter is usually unobtainable through macromolecular structure determination by X-ray crystallography?
Select one:
the shape of the electron density throughout the molecular structure
the distances between protons
the position of atoms and bonds in a macromolecule
xyz coordinates for each atom in the molecule
X-ray crystallography is the most successful technique for determining the three-dimensional structure of biological macromolecules. To publish a scientific journal article describing the crystal structure it is generally a requirement that the structure is submitted to the Protein DataBank. All structures in the Protein DataBank are publicly available.
What parameter is usually unobtainable through macromolecular structure determination by X-ray crystallography?
Select one:
the shape of the electron density throughout the molecular structure
**the distances between protons**
the position of atoms and bonds in a macromolecule
xyz coordinates for each atom in the molecule
261
X-ray crystallography is the most successful technique for determining the three-dimensional structure of biological macromolecules. To publish a scientific journal article describing the crystal structure it is generally a requirement that the structure is submitted to the Protein DataBank. All structures in the Protein DataBank are publicly available.
What is the approximate number of structures deposited in the Protein DataBank?
Select one:
50,000
500,000
140,000
14,000
What is the approximate number of structures deposited in the Protein DataBank?
Select one:
50,000
500,000
**140,000**
14,000
