Which of the following pairs of bonds within a peptide backbone show free rotation around both bonds?
A) C = O and N - C
B) C = O and N - Cn
C) Cα - C
... [Show More] and N - Cα
D) N - C and Cα - C
E) N - Cα and N - C
D) N - C and Cα - C
Thr and/or Leu residues tend to disrupt an α helix when they occur next to each other in a protein because:
A) Steric hindrance occurs between the bulky The side chains
B) An amino acid like Thr is highly hydrophobic
C) Covalent interactions may occur between the Thr side chains
D) Electrostatic repulsion occurs between the Thr side chains
E) The R group of Thr can form a hydrogen bond
A) Steric hindrance occurs between the bulky The side chains
The α-keratin chains indicated by the diagram below have undergone one chemical step. To alter the shape of the α-keratin chains -- as in hair waving -- what subsequent steps are required?
A) Chemical oxidation and then shape remodeling
B) Shape remodeling and then chemical oxidation
C) Chemical reduction and then chemical oxidation
D) Chemical reduction and then shape remodeling
E) Shape remodeling and then chemical reduction
B) Shape remodeling and chemical oxidation
Determining the precise spacing of atoms within a large protein is possible only through the use of:
A) X-ray diffraction
B) Electron Microscopy
C) Light Microscopy
D) Molecular model building
E) Ramachandran plots
A) X-ray diffraction
Which of the following is LEAST likely to result in protein denaturation?
A) Altering net charge by changing pH
B) Disruption of weak interactions by boiling
C) Changing the salt concentration
D) Exposure to detergents
E) Micing with organic solvents such as acetone
B) Changing the salt concentration
Protein S will fold into its native conformation only when protein Q is also present in the solution. However, protein Q can fold into its native conformation without protein S. Protein Q, therefore, may function as a ____________ for protein S.
A) Ligand
B) Protein Precursor
C) Molecular chaperone
D) Structural Motif
E) Super secondary structural unit
C) Molecular chaperone
Which of the following statements concerning proteins is true?
A) They are a form of secondary structure
B) They are examples of structural motifs
C) They consist of separate polypeptide chains (subunits)
D) They have been found only in prokaryotic proteins
E) They may retain their correct shape even when separated from the rest of the protein
E) They may retain their correct shape even when separated from the rest of the protein
What important function do molecular chaperones perform?
A) Assemble protein subunits into quaternary structure
B) Transport proteins to either the plasma membrane or release them from cells to the extracellular space
C) Add cofactors, coenzymes, or prosthetic groups to proteins as they are synthesized
D) Move proteins from endoplasmic reticulum to the Golgi Apparatus
E) Fold proteins into native conformation
E) Fold proteins into native conformation
In most cases, protein folding is complex and inhibited by aggregation. Which statement is FALSE regarding protein folding?
A) As ΔS increases, ΔG increases
B) Chaperones of the heat shock classes do not promote folding, but rather inhibit aggregation
C) Enzymes promote the formation of proper disulfide linkages by eliminating improper folding
D) All proteins require the input of energy and the assistance of chaperones for folding
E) Secondary structures usually form first in fold
D) All proteins require the input of energy and the assistance of chaperones for folding
What is false when talking about the MOST important factor that drives the formation of secondary structure of proteins?
A) Hydrophobic residues are largely buried in the protein interior
B) The number of hydrogen bonds are maximized
C) The number of ionic interactions are maximized
D) The number of disulfide bonds are maximized
D) The number of disulfide bonds are maximized
Which statement is FALSE about silk?
A) Fibroin is the main protein in silk
B) Make from different antiparallel β sheet structures
C) Make from different α sheet structures
D) Structure is stabilized by: H bonding and London forces
E) Small size change (Ala and Gly) allow the close packing of sheets
C) Make from different α sheet structures
The interactions of ligands with proteins:
A) are relatively nonspecific.
B) are relatively rare in biological systems.
C) are usually irreversible.
D) are usually transient.
E) usually result in the inactivation of the proteins.
D) are usually transient.
In the binding of oxygen to myoglobin, the relationship between the concentration of oxygen and the fraction of binding sites occupied can best be described as:
A) hyperbolic.
B) linear with a negative slope.
C) linear with a positive slope.
D) random.
E) sigmoidal.
A) hyperbolic.
A D-amino acid would interrupt a α helix made of L-amino acids. Another naturally occurring hindrance to the formation of an α helix in the presences of:
A) a negatively charged Arg residue
B) a non polar residue near the carboxyl terminus
C) a positively charged Lys residue
D) a Pro residue
E) two Ala residues side by side
D) a Pro residue
Which of the following best represents the backbone arrangement of two peptide bonds?
A) Cα - N - Cα - C - Cα - N - Cα - C
B) Cα - N - C - C - N - Cα
C) C - N - Cα - Cα - C - N
D) Cα - Cα - C - N - Cα - Cα - C
E) Cα - C - N - Cα - C - N
E) Cα—C—N—Cα—C—N
Linus Pauling and Robert Corey found that the CON bond in the peptide link is intermediate in length (1.32 A) between a typical C-N single bond (1.49 A) and a C=N double bond (1.27A). They also found that the peptide bond is planar (al four atoms attached to the C-N group are located in the same plane) and that the two α-carbon atoms attached to the C-N are always trans to each other (on opposite sides of the peptide bond)
A) What does the length of the C-N bond in the peptide linkage indicate about its STRENGTH (comparing to the bond strength of the double bond and single bond) and its BOND ORDER (whether it is single, double, or triple)
The length of the C - N bond has an intermediate strength. It is not long enough to be a double bond or short enough to be a single bond. It is neither a single or double bond because of its resonance structure. It is not as weak as a single but not as strong as a double bond (it is intermediate).
Bond order and bond length indicate the type and strength of covalent bonds between atoms. Bond order and length are inversely proportional to each other: when the bond order is increased, length order is increased.
Linus Pauling and Robert Corey found that the CON bond in the peptide link is intermediate in length (1.32 A) between a typical C-N single bond (1.49 A) and a C=N double bond (1.27A). They also found that the peptide bond is planar (al four atoms attached to the C-N group are located in the same plane) and that the two α-carbon atoms attached to the C-N are always trans to each other (on opposite sides of the peptide bond)
B) What do the observations of Pauling and Corey tell us about the ease of rotation about the C-N peptide bond?
The bond is unable to rotate. Single bonds will rotate while double bonds do not rotate. While this is an intermediate bond, no rotation will occur as it is not quite a single bond. This is important because there is no rotation around the bond which will restrict the ability of it to fold and change its conformation.
Our growing understanding of how proteins fold allows researchers to make predictions about protein structure based on primary amino acid sequence data. Consider the following amino acid sequence:
Ile-Ala-His-Thr-Tyr-Gly-Pro-Phe-Glu-Ala-Ala-Met-Cys-Lys-Trp-Glu-Ala-Gln-Pro-Asp-Gly-Met-Glu-Cys-Ala-Phe-His-Arg
A) Where might bends or B turns occur?
The bend will occur between 5-8:
Tyr - Gly - Pro - Phe
This is because Gly - Pro are next to each other. This occurs primarily in areas with Beta turns (usually in groups of 4)
Our growing understanding of how proteins fold allows researchers to make predictions about protein structure based on primary amino acid sequence data. Consider the following amino acid sequence:
Ile-Ala-His-Thr-Tyr-Gly-Pro-Phe-Glu-Ala-Ala-Met-Cys-Lys-Trp-Glu-Ala-Gln-Pro-Asp-Gly-Met-Glu-Cys-Ala-Phe-His-Arg
B) Where might different intra chain disulfide cross-linkages be formed?
Intra-chain disulfide cross linkages might be formed between 13 Cys and 24 Cys. They form between the two cystines. The R-group of the cystine makes the covalent bonds.
Our growing understanding of how proteins fold allows researchers to make predictions about protein structure based on primary amino acid sequence data. Consider the following amino acid sequence:
Ile-Ala-His-Thr-Tyr-Gly-Pro-Phe-Glu-Ala-Ala-Met-Cys-Lys-Trp-Glu-Ala-Gln-Pro-Asp-Gly-Met-Glu-Cys-Ala-Phe-His-Arg
C) Assuming that this sequence is part of a larger globular protein, indicate the probable location (the external surface or interior of the protein) of the following amino acid residues: Asp, Ice, Ala, Gln, Lys.
The outer protein surface is polar while the interior of the protein is non-polar (due to the hydrophobic effect). These residues are non polar as the majority are non polar:
Asp (-)
Ile (non-polar)
Thr (polar)
Ala (non-polar)
Glu (polar)
Lys (+)
There are more hydrophilic residues than hydrophobic residues making this non-polar on the EXTERIOR SURFACE.
Protein A has a binding site for ligand X with a KD of 10-6 M. Protein B has a binding site for ligand X with a KD of 10-9 M
A) Which protein has a higher affinity for ligand X and why?
P(A): Kd = 10-6 M
P(B): Kd = 10-9 M
Since protein A is larger than protein B, protein A has a higher kd value than protein B. Therefore, Protein B has a higher infinity due to the inverse relationship of affinity and kd value.
Protein A has a binding site for ligand X with a KD of 10-6 M. Protein B has a binding site for ligand X with a KD of 10-9 MB) Convert KD to KA for both proteins.
Kd and affinity have an inverse reaction, so a smaller kd = high affinity. This inverse relationship will allow us to use the equation:
P(A) Ka 1/10^-6 = 10^6
P(B) Ka 1/10^-9 = 10^9
What is the effect of the following changes on the O2 affinity of hemoglobin?
A) A drop in the pH of blood plasma to 7.4 - 7.2
Decrease
What is the effect of the following changes on the O2 affinity of hemoglobin?
B) An increase in the pH from 7.4 to 7.6
increase
What is the effect of the following changes on the O2 affinity of hemoglobin?
C) A decrease in the partial pressure of CO2 in the lungs from 6kPa (holding one's breath) to 2 kPa (normal).
Increases
As the pH drops, the O2 affinity also drops
What is the effect of the following changes on the O2 affinity of hemoglobin?
D) An increase in the BPG level from 5mM (normal altitudes) to 8mM (high altitudes).
Decreases
As the BPG levels increase, the O2 affinity decreases.
What is the effect of the following changes on the O2 affinity of hemoglobin?
An increase in CO from 1.0 parts per million in a normal indoor atmosphere to 30 ppm in a home that has a malfunctioning or leaking furnace
Decreases
As the CO concentration increases, the O2 affinity of hemoglobin decreases and that of CO affinity of hemoglobin increases.
Three membrane receptor proteins bind tightly to a hormone. Based on the data in the table below,
A) what is the Kd for hormone binding by protein 2
The Kd for hormone binding by protein 2 is ~0.5nM
Three membrane receptor proteins bind tightly to a hormone. Based on the data in the table below,
B) Which of these proteins bind most tightly to this hormone?
Protein 2 will bind most tightly to this hormone. The less dissociation, the stronger the binding between a molecule and its ligand. Since protein 2 has the least kd, it is stronger than the other two proteins. [Show Less]