Chapter #4 + #5 -- Biochemistry I
What is the mechanism for protein denaturation by extreme heat?
disrupting hydrogen bonding
What is the mechanism for protein denaturation by organic solvents and detergents?
disrupting nonpolar amino acid side chain interactions
The binding of ATP to a myosin head group causes:
disruption of the actin‑myosin interaction.
Which formation is NOT a stable, prominent, or widely occurring secondary structure?
disulfide bonds
Which interaction is NOT one of the forces that stabilize antibody‑antigen binding?
disulfide bonds
Individuals with sickle cell anemia:
need to inherit two copies of the mutated globin gene to express the full disorder.
Which technique allows conformational changes, protein folding, and interactions with other molecules to be studied?
nuclear magnetic resonance (NMR)
Which technique determines the structure of a protein in solution?
nuclear magnetic resonance (NMR)
What is the name of the structure in the figure?
parallel β sheet
What are the chromophores detected by circular dichroism (CD) spectroscopy of a protein?
peptide bonds
Which of the chemical interactions does NOT stabilize the native conformation of a protein?
peptide bonds
As predicted by Pauling and Corey, peptide bonds are in the ________ configuration.
planar, trans
Which topic is NOT included in the Protein Data Bank (PDB)?
possible mutations
A scientist injects a viral protein coat (non-pathogenic) into a rabbit. The rabbit's immune system will likely:
produce polyclonal antibodies specific to the virus.
The function of helper T cells is to:
produce signaling proteins called cytokines.
Which of these amino acids introduces a kink into an α helix and is thus rarely found in one?
proline
Which property is NOT shared by all globular proteins?
proline residues required for peptide chain bending in folds
Protein A has a binding site for ligand L with a Ka of 105 M-1. Protein B has a binding site for ligand L with a Ka of 108 M-1. Which protein has the higher affinity for ligand L?
protein B
What is the result of protein denaturation?
protein precipitation
What is the first step in immunoblotting?
protein separation by gel electrophoresis
Which of these terms BEST describes the higher order structure of α‑keratin shown in the figure?
protofibril
What is the first step in an x‑ray crystallography study?
purifying the protein
If a disulfide bond connects two polypeptide chains in a protein, the highest level of protein organization this protein has is:
quaternary structure.
A protein found on the outer surface of a cell that recognizes and binds specific ligands, which then triggers changes inside the cell is called a/an:
receptor
What did Christian Anfinsen use to break the disulfide bonds in ribonuclease A?
reducing agent
Quaternary structure:
refers to an arrangement of tertiary protein subunits in a three‑dimensional complex.
Which of these is NOT a characteristic function of the globin family?
regulation of atherosclerosis
What was the accomplishment of John Kendrew's x‑ray crystallography studies in 1959?
the determination of virtually all the non-hydrogen atoms positions in the myoglobin protein structure
What does a Ramachandran plot show?
the effect of steric hindrance on the allowable dihedral angles for a protein backbone
What does the designation His F8 in myoglobin refer to?
the eighth residue in sixth α helix
In general, the protein conformation with the lowest free energy has:
the highest number of weak interactions.
Which part of the immune system triggers when a person is infected with coronavirus?
the humoral and cellular immune systems
What is the predominant factor in protein stability?
the hydrophobic effect
Which item is the predominant factor in protein stability?
the hydrophobic effect
What role does vitamin C play in the synthesis of collagen?
the hydroxylation of proline and lysine
What feature of a disease classifies it as a prion disease?
the infectious agent is a protein
Which of these statements best defines the term secondary structure with respect to proteins?
the local spatial arrangement of the main‑chain atoms in a segment of a polypeptide chain
Which factor is NOT a constraint for α helix formation?
the occurrence of histidine and alanine residues
Renaturation is a term that describes:
the refolding of an unfolded globular protein so as to restore its native structure and function.
The flat membranous vesicles surrounding a myofibril is called:
the sarcoplasmic reticulum.
What was Eva Nogales's and Kathleen Collins's major contribution to structural biology?
the structure of telomerase using cryo‑electron microscopy (cryo‑EM)
A regular secondary structure occurs in a protein chain segment when:
the φ and ψ angles are the same, or nearly so, throughout the segment.
Aggregated myosin molecules are called:
thick filaments.
All fibrous proteins:
are insoluble in water.
Which amino acid would MOST likely be found in the binding site of a protein whose ligand is a cation?
aspartate
The hydrolysis of ATP by actin serves what function?
assembles actin filaments
The protein myosin has how many subunits?
6
How many turns are there in a typical α helix with a length of 4.86 nm?
9
What is the difference between a family and a superfamily of proteins?
A family consists of proteins having similar primary structures and/or similar functions and tertiary structures, whereas a superfamily consists of families that do not have similar primary structures but do have similar functions and tertiary structures.
Which characteristic is NOT a searchable category in the Structural Classification of Proteins (SCOP2) database?
amino acid sequence
Collagen, a component of connective tissues, becomes more brittle with age due to:
an accumulation of covalent cross‑links.
What structural information does an NMR spectrum provide?
an energy absorption spectrum representing nuclei identity and their immediate chemical environment
If you had strep throat, which immune component would detect this bacterial infection?
antibodies
Which blood component is part of the humoral immune system?
antibodies
Which is the more stable β sheet: parallel or antiparallel?
antiparallel due to more linear hydrogen bonds
In 2013, the Nobel prize in chemistry went to a group of structural biologists. What was the significance of their contribution?
computational modeling for use in protein structure determinations
What resource is necessary to fully analyze data output from cryo‑electron microscopy (cryo‑EM)?
computer algorithms
A change in ________ changes the spatial arrangement of atoms in a protein, but does not involve the breaking of covalent bonds.
conformation
Myoglobin:
consists mostly of α helices.
The heme prosthetic group:
consists of protoporphyrin and an iron (II) ion.
The Bohr effect:
contributes to the binding of O2 by hemoglobin in the lungs and the release of O2 from hemoglobin in the tissues.
If you have a 250 Å protein with four subunits, which method would BEST help you determine how each subunit orients in relation to the others?
cryo‑electron microscopy (cryo‑EM)
If you have an extremely small sample of a purified multi‑subunit enzyme, which method would be best to determine the sample's structural class?
cryo‑electron microscopy (cryo‑EM)
If you wanted to perform structural studies with human telomerase enzyme, one of the largest molecular complexes in the cell, which method would be BEST?
cryo‑electron microscopy (cryo‑EM)
Which of these methods does NOT require comparison with the amino acid sequence for protein structure determination?
cryo‑electron microscopy (cryo‑EM)
Which technique generates the structure of a protein quick‑frozen in non‑crystalline ice?
cryo‑electron microscopy (cryo‑EM)
All of these diseases are examples of amyloidoses EXCEPT for:
cystic fibrosis.
If you had a tapeworm, which immune component would detect this parasitic intestinal infection?
cytotoxic T cells
Which blood component is part of the cellular immune system?
cytotoxic T cells
Which structure will NOT be found on a Ramachandran plot?
collagen double helix
What is the length of a polypeptide with 120 amino acid residues in a single, continuous α helix?
18 nm
Estimate the number of amino acids in a typical α helix that is 30 Å long.
20
Calcium has a dissociation constant of 3 × 10-6 M when bound to the receptor calmodulin. What is the Ka?
3 × 105 M
What is the ATP consumption for one myosin head in a muscle contraction lasting 1 minute if the power stroke rate is 5 cycles/second?
300 ATP
How many amino acids are in a 6.2 nm long α helix?
41
How many amino acids are in a 62 Å long α helix?
41
What is the effective distance of van der Waals forces as atoms approach each other?
0.3 nm to 0.6 nm
Which would be considered a typical value (in the average range) for the dissociation constant (Kd) of a protein‑ligand system?
10-9 M
Given that an α helix has 3.6 residues per turn and the rise along the α helix axis is 5.4 Å, approximately how many amino acids would you find in a single contiguous α helix that is 210 Å long?
140
Which of these atoms does NOT have the nuclear spin that gives rise to an NMR signal?
14C
What does "the unfolded state of a protein is characterized by a high degree of conformational entropy" mean?
A polypeptide chain has many conformations depending on the environment.
Which amino acid sequence maximizes ion pairing for the stabilization of α helix formation at pH 7?
ADVVKLIEVAR
Which statement is TRUE regarding the β conformation?
Adjacent polypeptide chains are either parallel or antiparallel regarding their amino‑to‑carboxyl orientations.
What happens when ATP binds to myosin?
After ATP hydrolysis, myosin releases F‑actin and binds to another F‑actin, shortening the sarcomere.
Which statement regarding Ramachandran plots is FALSE?
Alanine, with a ΔG° of 0 kJ/mol, is the amino acid found in nearly all of the conformation regions of the plot.
What statement does NOT describe one of the benefits of cryo‑electron microscopy (cryo‑EM)?
Analysis does not require state‑of‑the‑art computer resources.
Which statement regarding monoclonal antibodies is TRUE?
Antibodies synthesized by identical B cells bind the same antigen epitope.
Which statement is FALSE regarding the binding of 2,3‑BPG to hemoglobin?
BPG blood levels decrease in individuals shortly after they move from sea level to higher altitudes.
Which statement does NOT describe how hemoglobin compensates for the molecular issues surrounding iron‑bound oxygen transport?
Binding CO substantially increases oxygen affinity in the remaining subunits, decreasing the toxic effects.
The effect of pH on the binding of O2 to hemoglobin is called the:
Bohr effect.
Which statement regarding the effect of pH on oxygen binding to hemoglobin is TRUE?
Both O2 and H+ bind hemoglobin, but with inverse affinity.
What is the range of each angle plotted on a Ramachandran plot?
Both φ and ψ range from -180° to 180°.
Rotation about which bond changes the dihedral angle designated ω?
C-N
Which bond limits the range of conformations available for a polypeptide chain?
C-N
Which covalent bond is the shortest in adjacent amino acid residues arranged as Cα-C-N-Cα?
C-N
What metal ion is critical in muscle contraction?
Ca2+
Which ion serves as a signal from the nervous system for muscle contraction to begin?
Ca2+
Why are disulfide bonds typically found only in secreted, extracellular proteins and not usually observed in cellular proteins?
Cell interiors tend to be reductive, whereas cell exteriors tend to be oxidative.
How might an ion pair destabilize a protein?
Charged amino acids interact with water in the unfolded protein.
How does the solvation layer contribute to protein folding?
Clustered hydrophobic groups reduce the water's entropy, decreasing the solvation layer.
How does genetic engineering aid the translation of 2D NMR spectra into a 3D protein structure?
Comparing the original spectra to the genetically engineered spectra aids the individual signal assignments.
Which statement does NOT describe how computers aid structural biology studies?
Computers track protein folding in real time.
What happens when an antibody binds an antigen?
Conformational changes in the antibody and/or the antigen allow interaction between complementary groups.
Which statement does NOT explain why covalent bonds place the greatest rigidity on protein structure?
Covalent bonds are the most prevalent interaction in a protein.
Protein disulfide isomerases contain ________ residues, which undergo reversible oxidation‑reduction reactions while assisting a protein to adopt its most stable three‑dimensional structure.
Cys
Rotation about which bond changes the dihedral angle designated ψ?
Cα-C
Which sequence is MOST likely to form an α helix at pH 7?
DFAHYLEWAR
How do prion proteins cause disease?
Diseased prion proteins convert the two α helices in normal prions to amyloid-like β sheets.
Which statement is TRUE concerning disulfide bonds?
Disulfide bond formation is more likely outside of the cell.
Which statement is TRUE about disulfide bonds?
Disulfide bonds are not as common for proteins inside cells due to the reducing environment.
How do actin and myosin interact with each other?
Each actin monomer in the thin filament binds one myosin head group with high affinity.
Which statement does NOT describe one of the challenges for analyzing the structure of protein crystals using x‑ray crystallography?
Even large proteins are smaller than the wavelength of light, making resolution problematic.
What is the role of ATP hydrolysis in actin?
Every actin molecule complexes ADP during filament formation.
An arrow points to part of the immunoglobulin structure. What is the name of this portion of the structure?
Fab
The heme group contains ________, which binds oxygen.
Fe2+
Which statement regarding globular proteins is FALSE?
Fibrous proteins are more compact than globular proteins.
Why is iron bound to a heme used to transport O2 in blood, instead of simply using free iron (not bound to heme)?
Free iron promotes the formation of reactive and damaging hydroxyl radicals from O2.
What important discovery did William Asbury make in the 1930s?
He used x‑ray crystallography to demonstrate the regular structure of hair keratin.
________ are NOT a feature of skeletal muscle fibers.
Helicases
Which antibody is pictured?
IgM
How can cryo‑EM sort images or view different conformation states?
Images of single protein molecules depict their quaternary structure.
Why is the α helix the most stable protein structure?
Hydrogen bonds form between the hydrogen on the nitrogen and the fourth carbonyl oxygen.
Why is the sequence DFAHFWRYR unlikely to participate in an α helix?
Hydrophobic residues are too close together.
Which statement regarding protein structure is TRUE?
Hydrophobic side chains are usually in the interior of the native structure.
Which statement regarding protein structure is true?
Hydrophobic side chains are usually in the interior of the native structure.
Which statement is TRUE about a Hill plot?
If the slope is greater than 1, ligand binding is cooperative.
Which immunoglobulin contains a J chain in its structure?
IgA
Which immunoglobulin exists as either a monomer, dimer, or trimer in secretions such as saliva, tears, and milk?
IgA
Sometimes, the body elicits an immune response against allergens like pollen that it would normally reserve for pathogens. Which immunoglobulin is known for its role in the allergic response?
IgE
Which immunoglobulin binds to the pathogen and activates macrophages to engulf and destroy the whole antibody‑pathogen complex?
IgG
Why is the sequence KWGHFARYD unlikely to participate in an α helix?
Ion pairing disrupts helix formation when similarly charged amino acids are three residues apart.
Which statement regarding protein folding is FALSE?
Ionic interactions form in the final steps of protein folding.
Which statement does NOT describe a characteristic of a peptide bond?
It causes resonance stabilization of each backbone bond.
Which statement does NOT describe one of the benefits of using cryo‑electron microscopy (cryo‑EM) for protein structure analysis?
It detects proteins in solution.
Which statement regarding structural biology is FALSE?
It enables protein sequence determinations based on protein function.
Which statement about myoglobin is FALSE?
It has four sites to bind oxygen.
Which statement is true regarding troponin C?
It has two calcium‑binding domains.
How does TOCSY compliment NOE in the translation of 2D NMR spectra into a 3D protein structure?
It identifies which NOE signals represent atoms linked by covalent bonds.
Which statement does NOT describe one of the benefits of using NMR spectroscopy for protein structure analysis?
It images large molecular complexes.
Which statement describes a solvation layer for a hydrophobic protein solute?
It is a highly ordered, low‑entropy layer of water surrounding a solute.
Which statement is TRUE regarding hemoglobin?
It is a symmetric oligomer.
What is the best way to characterize the structure shown?
It is an antiparallel β sheet.
Which statement is TRUE about using the Hill equation?
It is possible to observe negative cooperativity.
Which statement does NOT describe one of the benefits of x‑ray crystallography?
It needs very small amounts of purified protein.
Which statement does NOT describe a benefit of molecular dynamics simulations?
It provides hard evidence for the dynamics of protein folding.
Which statement about protein folding is FALSE?
It requires protein disulfide and peptide prolyl cis‑trans isomerases.
How does a vaccine protect against a virus?
It stimulates the production of memory cells, which generate a rapid immune response upon subsequent infection.
Protein A has Ka = 6.0 μM-1 for binding ligand L, and protein B has Kd = 4.0 μM for binding L. Based on this information, which statement is TRUE?
The Ka of protein B for L is 0.25 μM-1.
Suppose a mutant form of Hb were found that could not bind to 2,3‑BPG as effectively. What might the effect be on the O2 binding for this Hb?
It would increase O2 affinity.
What is unique about a proline residue that is part of a β turn?
Its N‑terminal peptide bond is cis.
What structural feature distinguishes fibroin from other fibrous proteins?
Its polypeptide chains are predominantly in the β conformation.
When half of the binding sites are occupied by ligand, the concentration of ligand equals:
Kd.
What is the general hierarchy of protein folding?
Local structures form before long‑range interactions.
What are the implications of myoglobin's hyperbolic oxygen binding curve and hemoglobin's sigmoidal oxygen binding curve?
Myoglobin functions as an oxygen storage protein and hemoglobin functions as an oxygen transport protein.
Which statement about myoglobin is FALSE?
Myoglobin is a relatively large, oxygen‑binding protein.
What does the term power stroke mean?
Myosin returns to its original resting state, and actin pulls the myosin tail towards the Z disk.
Rotation about which bond changes the dihedral angle designated φ?
N-Cα
If you have a solution containing a purified protein and its labeled ligand, which method would be BEST for characterizing the protein's binding site?
NMR spectroscopy
Are all denatured proteins able to refold properly when returned to native conditions?
No, although small stable proteins refold spontaneously, most proteins require assistance.
Are properly folded proteins completely stable?
No, regions of low stability may allow a protein to alter its conformation between two or more states, enabling protein function.
Which statement about oxygen‑binding proteins is FALSE?
O2 binding to myoglobin is allosteric but not cooperative.
Which statement regarding peptide bonds is FALSE?
The N atom in a peptide bond has a partial positive charge.
How does sickle cell anemia change the conformation of hemoglobin, and what effect does this have on oxygen binding?
Oxygen binding decreases because deoxygenated HbS aggregates and distorts erythrocytes.
How does cooperative binding enable hemoglobin to transport oxygen efficiently?
Oxygen binding to one subunit enhances the affinity for additional oxygen binding to the other subunits.
Why do humans need hemoglobin as an oxygen carrier?
Oxygen has a low solubility in blood plasma.
Which disease is caused by misfolded α‑synuclein protein?
Parkinson's disease
Which of these amino acids would be part of the hydrophobic core of a protein?
Phe
What happens to polar groups on the interior of a folded protein?
Polar groups participate in hydrogen bonds or ionic interactions.
What characterizes polyclonal antibodies?
Polyclonal antibodies recognize different epitopes on the same antigen.
Why is the sequence DCVPAIPSQR unlikely to participate in an α helix?
Proline residues cause kinks in the helix.
Protein A has a Ka of 6.0 μM-1 for binding ligand L, and the protein B has a Kd = 4.0 μM for binding ligand L. Based on this information, which statement is true?
The Ka of protein B for L is 0.25 μM-1
What is Levinthal's paradox?
Protein folding is not a completely random, trial‑and‑error process, as the time required for a single molecular vibration for each amino acid residue is too great.
How is the immune system able to recognize and deal with all of the different disease-causing agents in the world?
Random genetic recombination of immunoglobulin gene segments creates a huge, diverse antibody pool.
How does molecular motion affect the binding of O2 to myoglobin?
Rapid molecular flexing of the amino acid side chains produces transient cavities, allowing O2 access to the ligand‑binding site.
Which statement regarding immunoglobulin binding and specificity for the antigen is FALSE?
Receptors on the Fc region surface recognize and bind the antigen.
Which statement is TRUE regarding salt bridges?
Salt bridge strength is greater in hydrophobic environments than in polar environments.
Which statement is TRUE regarding the interactions contributing to a protein's conformation?
Secondary, tertiary, and quaternary protein structure depends on weak interactions.
Which of the amino acids would be located on the exterior of a protein and not part of the hydrophobic protein core?
Ser
Which statement is FALSE?
Some small molecules bind hemoglobin with greater affinity than oxygen.
Which statement is FALSE?
Stable proteins maximize the number of unpaired hydrogen-bonding and ionic groups.
Why do intrinsically disordered proteins often function as regulators or hubs for signaling pathways?
Structural flexibility allows interaction with many different proteins.
What is the response that takes place once IgE binds an antigen?
The Fc region binds to basophils and mast cells, triggering phagocytosis and histamine release.
What is the response that takes place once IgG binds an antigen?
The Fc region binds to macrophages, triggering phagocytosis.
IgG can bind to viruses that invade an organism. What happens next?
The Fc region of IgG binds to a macrophage, which destroys the virus.
Which statement is NOT one of the important conclusions from the original myoglobin structure studies?
The accessibility of heme allows for free oxidation from the ferric to ferrous form.
How does working skeletal muscle exemplify two common molecular protein functions: protein‑ligand interaction and enzyme?
The actin‑myosin interaction is a protein‑ligand interaction and myosin acts as an ATPase.
Which statement about the myoglobin structure is TRUE?
The backbone consists of eight segments of α helix.
Which statement is TRUE about antibody‑antigen binding?
The binding involves many noncovalent weak interactions between the antigen and antibody, so the Kd for this process is very low.
Why is arterial blood bright red and venous blood dark purple?
The binding of O2 changes the electronic properties (but not the oxidation state) of the ferrous ion in the heme.
Why are peptide bonds considered to have partial double bond character?
The carbonyl oxygen and the amide nitrogen resonate by sharing electrons, creating a small electric dipole.
Some mutations can reduce protein stability, but not completely destroy it. In the Siamese cat, a G→R transition, changing glycine to arginine (G302R), makes the tyrosinase enzyme in skin cells sensitive to temperature. This enzyme takes part in the synthesis of melanin, the dark pigment in hair and skin. It is properly folded at low body temperatures but denatured at high body temperatures. What can we then say about the Siamese cat?
The dark areas around its paws, nose, and ears are slightly cooler than the rest of the cat.
Which statement regarding the Protein Data Bank (PDB) is FALSE?
The database only contains protein structural information.
What is one of the many important conclusions from the original myoglobin structure studies?
The dense hydrophobic core is stabilized by the hydrophobic effect and enhanced by short‑range van der Waals interactions.
Which statement describes how protein structure and conformation affect the binding of small molecules to myoglobin?
The distal His hydrogen bonds with the polar Fe-O2 complex to stabilize the complex and increase oxygen affinity.
Which statement regarding oxygen binding to hemoglobin is TRUE?
The electronic properties of heme iron changes, altering the color of the blood.
Why does silk not stretch even though it has a flexible structure?
The extended β conformation prevents stretching, whereas extensive hydrogen bonding and van der Waals forces allow for flexibility.
Which statement is TRUE about the binding of O2 or CO to free heme in comparison to the binding to heme associated with myoglobin?
The heme in myoglobin has enhanced binding of O2 as compared to free heme.
Why do improperly folded proteins pose a problem for cells?
The hydrophobic residues are exposed, leading to aggregates that could have alternate, disease‑laden activity.
Why are salt bridges much stronger when they occur at the interior of a protein as compared to its surface?
The interior of the protein has a much lower dielectric constant than the solvent, so there is no shielding of the charges.
Why are fibrous proteins difficult to study using x‑ray crystallography?
The molecules are aligned side by side, but not all are oriented in the same direction.
What is the relationship between the noncovalent bonding observed in protein folding, free energy, and stability?
The number of noncovalent bonds is directly related to ΔG and stability.
Which statement is TRUE regarding type I and type II β turns?
Type I turns occur more frequently than type II turns.
You just identified a novel protein and generated a primary antibody for it. Which analytical method would you choose to determine whether this protein exists in a particular blood sample?
Western blot
Leghemoglobin is an oxygen-binding protein in root nodules that contain bacteria and fix atmospheric nitrogen. Which statement is true if leghemoglobin is like myoglobin and not hemoglobin?
The oxygen-binding curve is hyperbolic.
Which statement is TRUE regarding parallel β sheets?
The parallel conformation contains the amino‑to‑carboxyl orientations in the same direction.
What does a circular dichroism (CD) spectroscopy signal indicate?
The peptide bond is in a folded environment.
Which statement does NOT explain why the stability of a protein is not simply the sum of the weak interaction free energies?
The primary structure dictates exactly how the protein must fold.
Which statement describes a destabilizing effect on a hydrophobic protein core?
The protein folds so that its hydrophobic groups are on the interior, encompassing three hydrophilic groups.
What does it mean for two proteins to be in the same protein family?
The proteins either have similar primary structures and/or similar functions and tertiary structures.
Which statement regarding the chaperonins is FALSE?
The proteins have a molecular weight near 70 kDa.
Which statement is TRUE regarding the oligomeric protein hemoglobin?
The quaternary structure consists of two α subunits and two β subunits.
What is the mechanism of denaturation when ribonuclease A incubates with urea and a reducing agent?
The reducing agent cleaves the disulfide bonds and urea disrupts the hydrophobic effect.
Which statement does NOT reflect one of the changes involved in the T→R transition as oxygen binds hemoglobin?
The space between α subunits widens.
What is the problem with generating one‑dimensional NMR spectra?
The spectrum is too complicated for analysis.
Which statement regarding the tertiary structure of proteins is FALSE?
The tertiary structure of a protein is destabilized by the hydrophobic effect.
Which statement regarding the φ and ψ dihedral angles is FALSE?
The φ and ψ dihedral angles can have any value between -180° and +180°.
What does the "T" in T cells mean/indicate?
Their latter stages of development occur in the thymus.
In aqueous solution, proteins tend to fold and bury the hydrophobic amino acids towards the protein's interior. In the process, the protein loses a great deal of conformational entropy as it adopts a more ordered shape. If the protein loses so much entropy, why does it fold?
There is a larger entropic gain for the surrounding water molecules.
Which statement regarding the Hsp70 protein family is FALSE?
These proteins are necessary for the growth of some bacterial viruses.
How are the equilibrium association and equilibrium dissociation constants related?
They are reciprocals of each other.
Which statement is TRUE about salt bridges?
They are stronger in the hydrophobic interior of a folded protein than on the surface.
Which statement about motifs is FALSE?
They are very simple structures, representing only a small part of a protein.
How do "pharmacological chaperones" work?
They correct certain misfolding events in the membrane‑bound CFTR protein.
Which statement regarding helper T cells is FALSE?
They directly destroy infected cells and pathogens.
Which characteristic is NOT one of the similarities between the hemoglobin and myoglobin structures?
They each have four subunits.
Which statement is TRUE about the side chains (R groups) of amino acids in an α helix?
They extend radially out from the helix.
What is the function of a chaperone protein?
They interact with partially folded or improperly folded polypeptides to facilitate correct folding pathways.
How do aromatic residues affect the formation of amyloid fibrils?
They stabilize the protein structure such that fibrils form more slowly and disease onset occurs later in life.
What conclusion can be drawn regarding a protein enriched with small and charged amino acids?
This protein may be water soluble, but it is disordered and not stable.
Do crystal structures give an accurate picture of the protein's true structure?
Yes, the crystal‑derived structure almost always represents a functional conformation of the protein.
What is a β turn?
a 180° structure involving four amino acids connecting the ends of two adjacent segments of an antiparallel β sheet
What happens immediately after ATP binds to myosin?
a cleft in the myosin molecule opens, disrupting the actin‑myosin interaction to release the bound actin
What is a topology diagram?
a comparison of structural folds and motifs that allows the visualization of protein secondary structure and interconnection
What is a Fourier transform?
a computer‑generated mathematical technique used in x‑ray crystallography
What happens immediately after the phosphate products of ATP hydrolysis releases from myosin?
a conformational change closes the myosin cleft, strengthening the binding interactions between myosin and actin
What is the Protein Data Bank (PDB)?
a growing archive of experimentally determined three‑dimensional structures of biological macromolecules
What does actin look like in muscle cells?
a long polymer filament consisting of monomers bound to ADP
A protein's ligand is:
a molecule that reversibly binds to the protein.
Which statement describes a prion?
a normally occurring protein that adopts a disease‑causing conformation
Which answer choice describes the quaternary structure of hemoglobin?
a pair of αβ protomers; four heme groups
What is tropomyosin?
a protein that blocks the myosin head group attachment site by binding to the thin filament
What is an electron‑density map?
a representation of protein structure constructed from the x‑ray diffraction pattern
What is the EMDataResource?
a searchable database containing protein structure maps
What is a hapten?
a small molecule linked to a protein that can be used in the laboratory to elicit an immune response
What is NOESY?
a two‑dimensional NMR technique measuring distance‑dependent coupling of nuclear spins in nearby atoms through space
What is TOCSY?
a two‑dimensional NMR technique measuring the coupling of nuclear spins in atoms connected by covalent bonds
Circular dichroism (CD) spectroscopy measures the difference between:
absorption of right circular polarized light and absorption of left circular polarized light.
Oxygen can be considered an ________ modulator of hemoglobin.
activating homotropic
The α helix is:
affected by the identities of the residues near each end
Which amino acid has the greatest tendency to form an α helix?
alanine
A ligand binds to a protein and enhances the binding of another ligand at a different binding site in the protein. The protein is classified as a/an ________ protein.
allosteric
What is the mechanism for protein denaturation by extreme pH?
altering the net charge on a protein
What is crowdsourcing in structural biology?
background software on home computers that completes small portions of protein‑folding experiments
An arrow points to part of the immunoglobulin structure. What is the name of this portion of the structure?
basal fragment
Immunoglobulins:
bind tightly to their antigens.
How does urea denature proteins?
by disrupting hydrogen bonding and hydrophobic interactions
How does a structural biologist confirm the presence of α helices in an NMR spectrum?
by identifying certain patterns of NOE signals
Molecules that assist the folding of proteins are called:
chaperones
Which feature is NOT associated with globular proteins?
classified as either all α or all β
The process stimulated by helper T cells that selectively stimulates the proliferation of cytotoxic T cells and B cells that can bind to a particular antigen is called:
clonal selection.
Autophagy of amyloid fibers includes:
degradation by encapsulation followed by docking with a lysosome.
Denaturing followed by renaturing of a protein:
demonstrates that primary structure dictates tertiary structure.
Circular dichroism (CD) spectroscopy can do all of the following EXCEPT:
determine the primary structure of proteins.
Which factor will NOT denature proteins?
dialysis
The coiled coils of the keratin molecule are covalently attached to adjacent coils in a reaction that can be reversed using mild reducing agents. What type of cross‑links might be involved in covalently linking the keratin fibers?
disulfide linkages between Cys and Cys side chains
A ________ is a part of a polypeptide chain that is independently stable or could undergo movement as a single entity with respect to the entire protein.
domain
A specific molecular structure within an antigen that is recognized and bound by an antibody or T-cell receptor is called its:
epitope
The particular chemical group or groups in a macromolecule to which a given antibody binds is BEST defined as the:
epitope
Which cells do NOT participate in immunity?
erythrocytes
Which atom or molecule does NOT modulate oxygen binding to hemoglobin?
ferrous iron
A protein that consists of mostly one type of secondary structure, has a relatively simple tertiary structure, and whose function is to provide structural support is likely a ________ protein.
fibrous
The mammalian cell division protein p27 has a flexible structure that allows it to inhibit several different enzymes. What type of protein is p27?
intrinsically disordered
Most binding sites:
involve a cleft arranged within the protein for highly specific ligand binding.
Which of the terms describes the thermodynamic process of converging many conformational options to a single native conformation?
free‑energy funnel
Which disease is caused by the tau protein?
frontotemporal dementia and parkinsonism
Polypeptides that are folded into a roughly spherical shape and may contain several types of secondary structure are classified as ________ proteins.
globular
Which amino acids are particularly common in β turns?
glycine and proline
A newly discovered protein has multiple subunits, each with a single ligand-binding site. Binding of ligand to one site increases the binding affinity of other sites for the ligand. The Hill coefficient (nH) is:
greater than 1
Collagen
has fibrils consisting of cross‑linked triple helices of polypeptide chains.
What is carboxyhemoglobin?
hemoglobin with bound carbon monoxide
An arrow points to part of the immunoglobulin structure. What is the name of this portion of the structure?
hinge
Mast cells produce:
histamine
Which of these chemical interactions plays a large role in maintaining the secondary structure of proteins?
hydrogen bonds
Reverse turns are classified as secondary structure because:
hydrogen bonds between backbone amide groups stabilize them.
A good way to predict whether an amino acid side chain is on the outside or inside of a protein is to consider its ________.
hydropathy (polarity)
Which type of chemical interaction contributes the MOST to the stability of most proteins?
hydrophobic interactions
Which shape applies to a plot of the fraction of binding sites occupied with a ligand (Y) versus the concentration of ligand (L)?
hyperbolic
Which immune component binds bacteria, viruses, or large molecules identified as foreign and targets them for destruction?
immunoglobulins
Which factor increases the affinity of hemoglobin for oxygen?
increasing pH
The process of a protein changing conformation to better bind a ligand is called:
induced fit.
Which phenomenon is NOT an example of a van der Waals interaction?
ionic interactions that form a salt bridge
The β sheet:
is primarily stabilized by hydrogen bonds.
Which answer choice describes collagen?
left‑handed helix; forms triple‑stranded fibers wrapped in a right‑handed fashion
What structural conformation resides in the upper right-hand corner of the Ramachandran plot?
left‑handed α helix
Which type of globin is NOT found in humans and other mammals?
leghemoglobin
What does myosin look like in muscle cells?
long rod‑like bipolar structures with globular domains projecting from both ends
Which statement defines denaturation of a protein?
loss of tertiary structure sufficient for loss of function
Which answer choice is NOT a characteristic of unstructured proteins?
low charge density
Which of the conditions does NOT result in protein destabilization?
low free energy and maximum weak interactions
What is the result of applying a strong, static magnetic field to a solution containing a single type of macromolecule?
magnetic dipoles align either in parallel or antiparallel orientations
If you found a novel protein that has similarities to seven transmembrane G proteins, which method would be BEST to suggest possible protein folding patterns?
molecular dynamics simulations
Which experimental method is NOT used in structural biology?
molecular dynamics simulations
The computer analyzing NMR data requires several parameters. Which parameter is NOT necessary for generating a 3D protein structure?
molecular vibrations
NMR generated structures contain a degree of uncertainty due to:
molecular vibrations.
A Western blot can detect the presence of antigens and provides information about a protein antigen's:
molecular weight.
What type of antibody comes from a clone and recognizes a single epitope?
monoclonal
Which description is associated with immunoglobulin G?
most abundant immunoglobulin
What skeletal muscle unit is a large multinucleated cell?
muscle fiber
Which of these skeletal muscle structures is the largest?
muscle fiber
Which of these substances is NOT made of fibrous protein?
myoglobin
During muscle contraction, which protein hydrolyzes ATP?
myosin
In skeletal muscle tissue, the thick filaments are composed of:
myosin
Which molecule does NOT participate in thin filament formation?
myosin
The binding of ATP is important in the muscle contraction cycle to disrupt the actin‑myosin interaction. Where does the ATP bind?
myosin head group
What happens immediately after ATP hydrolyzes after binding to myosin?
myosin's conformational changes to a "high-energy" state allowing it to weakly bind an F‑actin subunit closer to the Z disk
A protein in a functional conformation is called a ________ protein.
native
What happens during the power stroke of the muscle contractility cycle?
return of myosin to its original resting state, allowing actin to pull the myosin tail towards the Z disk
What conditions are required for protein renaturation?
return to native conditions
What structural conformation resides in the lower left‑hand corner of the Ramachandran plot?
right‑handed α helix
Which structural conformation does NOT reside in the upper left‑hand corner of the Ramachandran plot?
right‑handed α helix
Which disease is characterized by the general degeneration of connective tissue and caused by a vitamin C deficiency?
scurvy
The Ramachandran plot:
shows combinations of permissible dihedral angles in a polypeptide chain.
Which of the forces does NOT guide the formation of a folded protein?
solubility
Which feature does NOT enhance protein stability in extreme heat?
stronger peptide bonds between amino acid residues
Which protein characteristic is NOT associated with proteostasis?
structure
The spontaneous renaturation of ribonuclease demonstrates that:
tertiary structure is determined by the primary structure.
Regarding the models of cooperativity:
the T state is low affinity and the R state is high affinity.
The backbone of a polypeptide chain can be pictured as a series of rigid planes, with consecutive planes sharing a common point of rotation at ________.
the alpha carbon
Cooperativity refers to:
the characteristic of a protein in which binding of the first molecule of a ligand changes the affinity for the second molecule.
What is proteostasis?
the continuous maintenance of an active set of cellular proteins
What is the role of peptide prolyl cis-trans isomerase (PPI)?
to catalyze the interconversion of the cis and trans isomers formed by Pro residues
Why did Christian Anfinsen incubate ribonuclease A with urea and a reducing agent?
to cleave the disulfide bonds and disrupt the hydrophobic interactions
Why was the ribonuclease A denaturation experiment repeated with a chemically synthesized enzyme?
to eliminate the possibility that an impurity in the native enzyme enabled refolding
What is the role of protein disulfide isomerase (PDI)?
to exchange specific covalent bond formation until the proper native conformation forms
Which proteins regulate skeletal muscle contraction so that it only occurs in response to appropriate signals from the nervous system?
tropomyosin and troponin
Which proteins regulate the interaction between actin and myosin so that skeletal muscle contraction occurs only in response to appropriate signals from the nervous system?
tropomyosin‑troponin complex
What prevents the binding of myosin to actin in skeletal muscle?
troponin I
By definition, quaternary structure is exhibited by proteins that have:
two or more separate, but associating, protein chains.
If you have two forms of the same water‑soluble protein, one of which contains 13C, which method would be BEST for structural characterization?
two‑dimensional NMR spectroscopy
Which of these diseases is NOT associated with protein misfolding?
type 1 diabetes mellitus
What did Christian Anfinsen use to disrupt the stabilizing hydrophobic effect in ribonuclease A?
urea
Which description does NOT apply to β turns?
usually involves three amino acids
A deficiency of which vitamin leads to problems with collagen synthesis?
vitamin C
If you had a keratinaceous horn sample from an unknown species, which method would be BEST for structural determinations?
x‑ray crystallography
If you have a large sample of a protein whose molecules align side by side, oriented in the same direction, which method would be BEST for structural determinations?
x‑ray crystallography
Which technique determines the spacing of atoms in a crystal lattice?
x‑ray diffraction
Which statement is NOT a rule governing the physical and chemical constraints of protein folding?
α helices are generally left‑handed.
Which molecule belongs to the family of intermediate filament (IF) proteins?
α‑keratin
The ________ is NOT an example of a type of protein secondary structure
α‑turn
Which distinctive feature does NOT differentiate collagen from α‑keratin?
β conformation chains
Which answer choice is an example of a complex motif made up from a simple motif?
β-α-β loops → α/β barrel
