Bio Chem MCQ Flashcards
- Which of the following best describes the characteristics of polar amino acids? 1-4-20
A. ionizable in water
B. more likely to be exposed to water than to be found in the interior of a folded protein
C. partially charged due to the oxygen atom in their carboxyl group
D. partially charged due to fairly consistent sharing of electrons among atoms in their R group
E. positively charged
Answer B: Polar amino acids are defined as those whose R groups are capable of forming hydrogen bonds
with water. Due to this property, they are also said to be hydrophilic (water loving) and, therefore, are most
often found exposed to the aqueous environment on the surface of proteins as opposed to buried in the
interior
- Which one of the following amino acids may be considered a hydrophobic amino acid at physiological pH
of 7.4? 1-5-2
A. arginine
B. aspartic acid
C. glycine
D. isoleucine
E. threonine
Answer D: Hydrophobic amino acids are those with side chains that do not like to reside in an aqueous
environment. For this reason, these amino acids are more often found buried within the hydrophobic core of
a protein, or within the lipid portion of a membrane
- The greatest buffering capacity at physiological pH would be provided by a protein rich in which of the
following amino acids?
A. alanine
B. cysteine
C. histidine
D. proline
E. tyrosine
Answer C: Histidine contains an imidazole ring as its R group. The nitrogen in this ring possesses a pKa around
6.0, thus it is able to accept or donate a proton at physiological ph. This fact makes the amino acid an ideal
buffering component of a protein containing several
Histidine residues
- You are studying a cell line derived from a liver tumor. This cell line expresses a mutated form of glycerol
kinase. Which of the following lipid classes is most likely to be found at reduced levels in this cell line due to
this gene defect? 9-4-12
A. cholesterol
B. fatty acids
C. phospholipids
D. sphingolipids
E. triglycerides
Answer E: Triglycerides are composed of a backbone of glycerol to which 3 fatty acids are esterified. One of
the pathways to triglyceride synthesis in hepatocytes is initiated by the phosphorylation of glycerol via the
action of glycerol kinase. Therefore, a defect in glycerol kinase activity in these cells would result in reduced
capacity to synthesize triglycerides.
- Certain nucleic acids harbor significant free energy that can be released and coupled to the synthesis of
biological molecules. Which of the following represents a nucleic acid form containing the greatest amount
of free energy?
A. adenine
B. adenosine
C. adenosine monophosphate
D. adenosine diphosphate
E. adenosine triphosphate
Answer E: The high free energy in nucleic acids is imparted by the formation of phosphate bonds. The
nucleobase and nucleosides do not contain sufficient energy to drive biosynthetic processes. The phosphate
in a monophosphate nucleotide is linked via an ester bond to the ribose. The di- and tri-phosphates of
nucleotides are linked by anhydride bonds. Acid anhydride bonds have a high ΔG0′ for hydrolysis imparting
upon them a high potential to transfer the phosphates to other molecules. Since the triphosphate nucleotide
contains 2 phosphoanhydride bonds, it is this form that has the greatest level of free energy.
- When glucagon binds to its receptors on the surface of adipose tissue, it activates a signaling cascade
leading to the release of free fatty acids that can be utilized by the liver and other peripheral tissues for energy
production. Which of the following is the correct nucleic acid involved in the triggering of this cascade? 7-1-4
A. ATP
B. cAMP
C. cGMP
D. GTP
E. xanthine
Answer B: Glucagon binds to plasma membrane receptors coupled through a G-protein that activates
adenylate cyclase. Adenylate cyclase generates cAMP from ATP and the resultant increases in cAMP in turn
activate cAMP-dependent protein kinase, PKA. Activation of PKA leads to increased fatty acids release from
triglycerides stored in adipose tissue.
- The quaternary structure of a given protein is defined by which of the following? 1-4-24
A. linear order of the amino acids
B. ordered organization of secondary structures within the protein
C. organization of super-secondary structures within the protein
D. overall structure resulting from association of domains within the protein
E. structure resulting from the interactions between multiple polypeptide chains
Answer E: Quaternary structure is the protein structure resulting from the interaction of at least 2 protein
subunits in the functional protein.
- In an enzyme with a critical glutamic acid residue (Glu, E) in the active site, which of the following amino
acid substitutions would be expected to have the least effect on enzyme activity? 1-3-16
A. Arg
B. Asp
C. Lys
D. Ser
E. Tyr
Answer B: Since glutamic acid is a negatively charged amino acid at physiological pH, any other negatively
charged amino acid, such as aspartic acid, could potentially be substituted without significant loss of enzyme
activity.
- You are examining the lipid-interaction characteristics of a particularly hydrophobic protein. Mutational
studies with this protein have been designed to examine these lipid interaction properties. Addition of which
of the following amino acids to the protein would most likely be expected to interfere with the lipid-
interaction properties? 1-3-16
A. aspartate
B. glycine
C. isoleucine
D. leucine
E. valine
Answer A: Lipids would most likely interact with equally hydrophobic substances. Aspartic acid is an acidic
amino acid and as such would be more likely to interact with an aqueous environment than a hydrophobic
lipid one.
- You are examining digestive enzymes and their processes of activation. You have isolated a mutant form
of one particular enzyme and found that it remains inactive in a mixture of digestive juices. The wild-type
enzyme is normally activated by hydrolysis on the C-terminal side of Arg and Lys residues and you determine that the mutant enzyme contains Ser residues at these critical positions. Which of the following digestive enzymes is most likely responsible for activation of the wild-type enzyme in your studies?
A. aminopeptidase
B. carboxypeptidase
C. chymotrypsin
D. enteropeptidase
E. lysozyme
Answer D: Trypsin is a pancreatic digestive enzyme derived from proteolytic cleavage of the precursor protein
trypsinogen. Enteropeptidase is produced by cells of the duodenum. It is secreted from intestinal glands
called the crypts of Lieberkühn following the entry of ingested food passing from the stomach.
Enteropeptidase converts trypsinogen into its active form trypsin. Trypsin cleaves its target substrates on the
C-terminal side of Arg and Lys residues.
- You are studying the characteristics of membrane-associated proteins. You have isolated and
characterized both wild-type and mutant forms of a particular protein. The mutant protein does not remain
anchored in the plasma membrane. Which of the following properties results in membrane anchoring of the
wild-type protein and is likely defective in the mutant version? 6-2-48
A. disulfide bond formation between the protein and its phosphatidylinositol anchorB. extensive hydrogen bonding of the amino acid side chains of the protein and the membrane phospholipid
tails
C. extensive hydrophobic interactions between the amino acid side chains of the protein and the membrane
phospholipid tails
D. formation of ionic bonds between the amino acid side chains and the phospholipid tails
E. formation of β-pleated sheet structures to maximize protein interactions with the phospholipid head group
B. extensive hydrogen bonding of the amino acid side chains of the protein and the membrane phospholipid
tails
C. extensive hydrophobic interactions between the amino acid side chains of the protein and the membrane
phospholipid tails
D. formation of ionic bonds between the amino acid side chains and the phospholipid tails
E. formation of β-pleated sheet structures to maximize protein interactions with the phospholipid head group
Answer C: Membranes are predominantly lipid and thus most likely to interact with hydrophobic amino acids.
The interaction between the hydrophobic R-groups of amino acids and the hydrophobic lipid tails of
membrane phospholipids anchors integral membrane proteins to the membrane.
- You are examining the thermodynamically stable structures of proteins. In particular you are studying the
α-helix and β-sheet conformations that form in the study proteins. These conformations correspond to which
of the following? 1-4-4
A. native conformation
B. primary structure
C. secondary structure
D. tertiary structure
E. quaternary structure
Answer C: The formation of secondary structures in proteins is the result of the order folding of groups of
amino acids into either α-helices or β-sheets.
- In the β-sheet structure of proteins, the hydrogen bond on the peptide bond nitrogen of one of the
peptides will most likely form a hydrogen bond with which of the following? 1-4-8/2021
A. hydrophilic side chains in the adjacent sheet segment
B. hydrophobic side chains in the adjacent sheet segment
C. peptide bond carbonyl in the adjacent sheet segment
D. peptide bond carbonyl within 3 amino acids of the same segment
E. water in the surrounding medium
Answer C: The formation of both α-helices and β-sheets is the result of the hydrogen bonds formed between
the hydrogen associated with the amide nitrogen of the peptide bond and the carbonyl oxygen of an adjacent
peptide bond.
- During the normal processes of the cell cycle, specific types of DNA–protein complexes form and
dissociate which allow condensation and decondensation of the chromosomes. Which of the following is the
major attractive force between the DNA and the proteins, allowing these complexes to form?
A. disulfide linkages
B. electrostatic interactions
C. hydrogen bonds
D. hydrophobic interactions
E. van der Waals forces
Answer B: DNA is very highly negatively charged due to the phosphate backbone of the nucleotides.
Therefore, DNA is most likely to interact with other molecules, such as proteins, via electrostatic interactions.
- You are studying the relationships between protein structure and function. You are most interested in
the characteristics of a family of proteins termed chaperones. Which of the following processes requires
chaperone activity in order to facilitate correct biological function? 1-5-17
A. assembly of coated pits
B. correct folding of nascent proteins
C. formation of tight junctions
D. interaction between actin and myosin
E. processing of telomeres
15. You are studying the relationships between protein structure and function. You are most interested in
the characteristics of a family of proteins termed chaperones. Which of the following processes requires
chaperone activity in order to facilitate correct biological function? 1-5-17
A. assembly of coated pits
B. correct folding of nascent proteins
C. formation of tight junctions
D. interaction between actin and myosin
E. processing of telomeres
Answer B: Chaperones are proteins that assist the noncovalent folding or unfolding and the assembly or
disassembly of other macromolecular structures, but do not occur in these structures when the structures
are performing their normal biological functions
- The peptide bond of all protein forms with highly specific orientation. This orientation contains atoms
linked in which of the following ways? 1-3-21
A. C-N-C-C
B. C-N-H-C
C. C-O-N-C
D. C-C-O-N
E. C-S-S-C
Answer A: The peptide bond is formed between the α-carbon of one amino acid and the α-amino nitrogen
of the adjacent amino acid, therefore the orientation of the atoms would be C-N. The second C in the correct
orientation is α-carbon of the C-terminal amino acid and the last C atom of the correct answer represents the
carbon of the carboxylic acid residue of the C-terminal amino acid in the peptide bond.
- You are studying the characteristics of protein secondary structure. You find that the protein you are
examining forms an α-helical structure more rapidly in an alcohol medium than it does in water. Which of the
following is the best explanation for this difference?
A. competition for hydrogen bonding is lower for ethanol than for water
B. ethanol forms covalent interactions with the peptide
C. hydrophobic forces are greater in ethanol than in water
D. the peptide aggregates in water but not in ethanol
E. van der Waals interactions are lower in ethanol than in water
Answer A: The α-helix results due to the formation of hydrogen bonds between adjacent amino acids in the
protein. Because these same atoms in the amino acids can form hydrogen bonds with water, there can be
competition for the formation of the bonds required for the α- helix. In the presence of ethanol there would
be less competition from the water molecules thus explaining the increased rate of α-helix formation in this
medium.
- You are studying the protein-folding characteristics of a particular protein. You find that under certain
conditions the protein does not fold correctly and it precipitates within the cytosol. Which of the following
processes is most directly responsible for aggregation and precipitation of the misfolded protein in the
cytoplasm? 1-4-20
A. attachment of palmitate to the C-terminus
B. exposure of hydrophobic residues on the surface of the proteinC. formation of incorrect disulfide bonds between pairs of cysteine residues
D. nonenzymatic glycosylation of amino groups by free glucose
E. phosphorylation of threonine or serine side chains
Answer B: The correct folding of proteins involves several different forces. One of the strongest forces is
hydrophobic interactions whereby, hydrophobic amino acids tend to be excluded from the aqueous surface
of proteins. The exposure of hydrophobic amino acids to the surface of a protein due to improper folding
could tend to lead to aggregation.
- Mutational studies on collagen proteins demonstrate that substitution of one particular amino acid
significantly affects the normal structure of the collagen molecules. Which of the following amino acids is
absolutely required for the stable formation of the collagen triple helix? 2-1-9
A. alanine
B. cysteine
C. glycine
D. phenylalanine
E. tryptophan
Answer C: All collagens contain 3-stranded helical segments of similar structure. The unique properties of
each type of collagen are due mainly to segments that interrupt the triple helix and that fold into other kinds
of 3-dimensional structures. The triple-helical structure of collagen arises from an unusual abundance of 3
amino acids: glycine, proline, and hydroxyproline. These amino acids make up the characteristic repeating
motif Gly-Pro-X, where X can be any amino acid. Each amino acid has a precise function. The side chain of
glycine, an H atom, is the only one that can fit into the crowded center of a 3-stranded helix. Hydrogen bonds
linking the peptide bond nitrogen of a glycine residue with a peptide carbonyl group in an adjacent
polypeptide help hold the 3 chains together. It is because of this role of glycine in collagen that it is
indispensable for normal collagen structure and function
- The parents of a 3-year-old boy bring him to the hospital following a fall as they are concerned, he has
broken his arm. His parents report that over the past year he has had several episodes of what they think is
uncharacteristically easy fractures in his legs from minor falls. They indicate that there is no family history of
bone disease. Physical examination shows bowing and deformities of the legs, and x-rays show evidence of
previous fractures and osteopenia. The physician suspects a collagen defect and orders a skin biopsy. The
results of the biopsy show unstable type I collagen that is due to a single-point mutation in one of the type I
genes. This mutation is most likely caused by which of the following amino acid substitutions in this patient?
1-5-17
A. Ala → Asp
B. Glu → Gln
C. Gly → Leu
D. Tyr → Trp
E. Ser → Phe
Answer C: The triple-helical structure of collagen arises from an unusual abundance of 3 amino acids: glycine,
proline, and hydroxyproline. These amino acids make up the characteristic repeating motif Gly-Pro-X, where
X can be any amino acid. The side chain of glycine, an H atom, is the only one that can fit into the crowded
center of a 3-stranded helix. Hydrogen bonds linking the peptide bond nitrogen of a glycine residue with a
peptide carbonyl group in an adjacent polypeptide help hold the 3 chains together. It is because of this role
of glycine in collagen that it is indispensable for normal collagen structure and function. Therefore, a mutation
causing a substitution of glycine for leucine would result in the production of defective collagen.
- An insoluble form of a prion protein accumulates in the brains of patients who have Creutzfeldt-Jakob
disease, CJD. Conversion of the normal soluble form of the prion protein to the pathologic insoluble form is
thought to involve conversion of α-helices to β-pleated sheets. In order for this structural transition to occur,
which of the following is most likely disrupted and reformed? 1-4-24
A. disulfide bonds
B. hydrogen bonds
C. peptide bonds
D. salt bridges
E. zinc fingers
Answer B: The α-helix and β-sheet structures in proteins result from the formation of hydrogen bonds
between the amide hydrogen of one peptide bond and an adjacent carbonyl oxygen in another peptide bond.
For an α-helix to convert into a β-sheet it is required that the hydrogen bonds holding the structure together
be broken and then a different series of hydrogen bonds need to form to generate the β-sheet structure.
- Eukaryotic ribosomes consist of 2 subunits designated as 40S and 60S. The S value is most dependent on
which of the following properties of the subunit? 4-3-18
A. composition of the RNA bases
B. interactions between the RNA and protein components
C. protein content
D. RNA content
E. shape and size of the subunit
Answer E: The “S” in 40S and 60S refers to the Svedberg coefficient, which is a unit of measure for
sedimentation rate. The sedimentation rate is the rate at which particles of an given size and shape travel to
the bottom of the tube under centrifugal force. The Svedberg coefficient is technically a measure of time and
offers a measure of particle size based on its rate of travel in a tube subjected to high gravitational force.
- When the malarial parasite invades a red blood cell, its metabolic waste products result in the acidification
of the cytoplasm. Which of the following best describes the consequences of this acidification on the activity
of hemoglobin (Hb)? 5-1-33
A. formation of carbaminohemoglobin is enhanced
B. hemoglobin tetramers become less stable and the complex dissociates
C. there is a shift to a more R state conformation
D. there is a shift to a more T state conformation
E. there is no effect from the acidification
Answering D: The principal negative regulator of the affinity of hemoglobin for oxygen is proton, H+. The
acidification of the erythrocyte cytoplasm by malarial parasite metabolism would be reflected by a significant
increase in [H+] which would, in turn, result in a higher level of T state hemoglobin.
- You are treating a patient who presents with microcytic anemia. Additional microscopic findings
demonstrate the presence of inclusion bodies in the red blood cells. Electrophoresis of erythrocyte protein
extracts shows a large excess of β-globins and a near complete lack of α-globins. Which of the following
disorders most closely correlates to your findings? 5-1-41
A. hemoglobin H disease
B. hereditary persistence of fetal hemoglobin
C. hydrops fetalis
D. sickle cell anemia
E. β-thalassemia major
Answer A: The α-thalassemias result when there is reduced expression at one or both of the α-globin genes.
In the α-thalassemias, normal amounts of β-globins are made. The β- globin proteins are capable of forming
homotetramers (β4) and these tetramers are called hemoglobin H, HbH. An excess of HbH in red blood cells
leads to the formation of inclusion bodies commonly seen in patients with α-thalassemia. In addition, the
HbH tetramers have a markedly reduced oxygen-carrying capacity. In β-thalassemia, where the β-globins are
deficient, the α-globins are in excess and will form α-globin homotetramers. The α-globin
homotetramers are extremely insoluble which leads to premature red cell destruction in the bone marrow
and spleen. Clinically this is referred to as hemoglobin H disease.
