Midterm 1 Flashcards
Which of the following can contribute to the function of a macromolecule?
a) Van der Waals interactions
b) Hydrogen bonds between
c) Electrostatic interactions
d) The type of covalent bonds between subunits of the macromolecule
e) All of the above
e) All of the above
Which of the following about protein secondary structure is FALSE?
a) An alpha helix depends on hydrogen bonding between amino acids in close proximity to one
another (located 3-4 amino acids apart in a protein).
b) A beta sheet depends on hydrogen bonding between amino acids that may be distant in the
linear sequence of a protein but close together in space.
c) A single protein may have some regions that adopt alpha-helix structure and other regions that
adopt beta-sheet structure.
d) The formation of a specific secondary structure like an alpha-helix in a region of a protein does
not depend on which amino acids are part of that region of the protein.
e) The secondary structure of a protein determines what kind of tertiary structure that protein will
have
d) The formation of a specific secondary structure like an alpha-helix in a region of a protein does
not depend on which amino acids are part of that region of the protein.
Grynate is a ligand for a protein called Thyminin. Which of the following about the interaction of
Grynate with Thyminin is FALSE?
a) The binding of Grynate to Thyminin involves non-covalent interactions.
b) The binding of Grynate to Thyminin will not be affected if the structure of Thyminin is changed so
that the position of amino acids involved in non-covalent interactions with Grynate is altered.
c) If a specific polar amino acid in Thyminin that is involved in a hydrogen bond with Grynate is
changed to a non-polar amino acid, this will reduce the affinity (strength) of the interaction of
Thyminin and Grynate.
d) The ability of Thyminin to bind Grynate is likely to be very specific; this does not necessarily
mean that Thyminin can also have other, unrelated molecules as ligands.
e) The binding of Grynate as a ligand to Thyminin is likely to be very specific; this does not
necessarily mean that Grynate can bind to other, unrelated proteins.
b) The binding of Grynate to Thyminin will not be affected if the structure of Thyminin is changed so
that the position of amino acids involved in non-covalent interactions with Grynate is altered.
A guanyl exchange factor (GEF) is a protein that
a) causes the covalent attachment of a phosphate (phosphorylation) directly to a serine amino acid
on a target protein.
b) causes the hydrolysis of GTP that is bound to a GTPase, so that the GTPase ends up being
bound to GDP as a direct result of the GEF.
c) leads to the binding of GTP to a GTPase, which leads to the GTPase being considered “active”
or in the on-state.
d) causes the removal of a phosphate group that was covalently attached to an amino acid on a
protein.
e) acts on Akt to cause Akt to become inactive
c) leads to the binding of GTP to a GTPase, which leads to the GTPase being considered “active”
or in the on-state.
Which of the following about cellular organelles is FALSE?
a) Peroxisomes are non-membrane bound organelles that are involved in cell metabolism (breakdown) of some lipids and carbohydrates.
b) The lysosome is a membrane-bound organelle that is causes the degradation of some types of proteins.
c) Endosomes are membrane-bound organelles that receive material from outside the cell and are involved in sorting.
d) Ribosomes are non-membrane-bound organelles that are responsible for synthesis of proteins.
e) Centrioles are non-membrane-bound organelles that control the formation of microtubules
a) Peroxisomes are non-membrane bound organelles that are involved in cell metabolism (breakdown) of some lipids and carbohydrates.
The appearance of chloroplasts during the evolution of some eukaryotes
a) occurred before the appearance of the nucleus in the eukaryotic lineage.
b) occurred due to the phagocytosis of cyanobacteria, which later resulted in endosymbiosis.
c) occurred before the appearance of the mitochondria in the eukaryotic lineage.
d) occurred because the evolution of chloroplasts allowed the eukaryotic cell’s own DNA to be
protected from damage during phagocytosis.
e) occurred before the appearance of enzymes that could synthesize lipids and make cell
membranes
b) occurred due to the phagocytosis of cyanobacteria, which later resulted in endosymbiosis.
Which of the following about formation of macromolecules is TRUE?
a) The primary structure of proteins is formed by hydrogen bonds between adjacent (neighboring)
amino acids.
b) The number of subunits that are covalently joined together to form a polysaccharide does not
matter for the function of the resulting polysaccharide.
c) The formation of glycosidic bonds between subunits in a polysaccharide must be coupled to the
hydrolysis of nucleoside triphosphates (e.g. ATP) in order to be favourable.
d) The synthesis of proteins involves a reaction that joins the amine of one amino acid to the R-
group of the next amino acid in the protein polymer.
e) If a specific protein has glutamate at the 6th amino acid position and valine at the 7th position,
then switching the position of these two so that the valine is at the 6th position and glutamate is
at the 7th position will not affect the structure of the protein.
c) The formation of glycosidic bonds between subunits in a polysaccharide must be coupled to the
hydrolysis of nucleoside triphosphates (e.g. ATP) in order to be favourable.
Which of the following about protein structure is FALSE?
a) Electrostatic interactions are not involved in tertiary structure of proteins, as these types of
interactions are only involved in secondary structure.
b) In an aqueous environment, non-polar amino acids are more likely to be in the interior of a
protein where they are not in contact with water.
c) A hydrogen bond interaction between the R-group of an amino acid in a protein and the R-group
of an amino acid on a separate protein contributes to quaternary structure.
d) A prion is a protein that has adopted a stable, abnormal configuration or structure, which in
some cases can lead to diseases such as mad cow disease.
e) If a protein has a specific type of structure in an aqueous solution, then that protein will likely
have a different structure when transferred to a non-polar solution
a) Electrostatic interactions are not involved in tertiary structure of proteins, as these types of
interactions are only involved in secondary structure.
Which of the following about eukaryotes and prokaryotes is TRUE?
a) Eukaryotes and prokaryotes both have a nuclear envelope (nucleus).
b) Early Eukaryotic cells were likely predatory and used phagocytosis to engulf and digest other,
smaller cells.
c) The last universal common ancestor was not yet able to make proteins as it did not have
ribosomes.
d) Prokaryotic cells have some membrane-bound organelles like an endoplasmic reticulum and a
Golgi apparatus to make proteins, but not others like peroxisomes and lysosomes.
e) Prokaryotes is a great new bubble tea place that opened up on Gerrard just east of Church.
b) Early Eukaryotic cells were likely predatory and used phagocytosis to engulf and digest other,
smaller cells.
Which of the following about the compound light microscope is TRUE?
a) Resolution refers to the amount of light (number of photons) that is detected when forming an
image at the eyepiece or detector.
b) The condenser collects the light after it has passed through the specimen.
c) Dark field microscopy results in formation of an image where bright regions represent light that
passed through the specimen without being scattered or reflected.
d) Increasing the magnification of an image always results in an increased resolution.
e) Phase contrast microscopy can increase the contrast in biological images and is based on
sample illumination with light that is entirely in phase before entering the sample.
e) Phase contrast microscopy can increase the contrast in biological images and is based on
sample illumination with light that is entirely in phase before entering the sample.
Fluorescence microscopy involves
a) illumination of a sample with light of a particular wavelength, followed by the formation of an
image by light emitted from the sample that has a smaller (shorter) wavelength.
b) use of an objective lens, which serves both to focus excitation light onto the specimen and to
collect light that is emitted by the fluorescent dyes in the specimen.
c) use of a microscope with a dichroic mirror that transmits light of both the excitation and
emission wavelengths, but reflects other light of wavelengths.
d) the same emission (second barrier) filter, a dichroic mirror, and an excitation (first barrier) filter
for every type of fluorescent dye in a sample, regardless of the dye’s emission wavelength.
e) use of an excitation filter (1st barrier filter) that eliminates light of all wavelengths other than light
emitted by fluorescent dyes in the sample.
b) use of an objective lens, which serves both to focus excitation light onto the specimen and to
collect light that is emitted by the fluorescent dyes in the specimen.
A confocal microscope
a) increases the resolution of an image by reducing the diffraction of light from objects in the
sample.
b) allows the illumination of only a small percentage of fluorescent dye molecules in a sample at a
time, so that after hundreds of images are obtained, a high-resolution image can be
reconstructed.
c) has an opaque plate near the detector, which has a small pinhole that removes most of the out
of focus light while allowing almost all of the in-focus light to reach the detector.
d) is able to eliminate out of focus light from an image using software, and thus occurs entirely after
the image has already been taken.
e) has a unique type of excitation filter that removes excitation light that is not in focus, so that only
fluorescent dyes that are in focus are able to absorb and emit fluorescent light.
c) has an opaque plate near the detector, which has a small pinhole that removes most of the out
of focus light while allowing almost all of the in-focus light to reach the detector.
Which of the following about the generation or use of antibodies that can be used in fluorescence
microscopy experiments is FALSE?
a) The injection of a purified protein into an animal like a mouse triggers an immune response and
a specific kind of B cell will undergo expansion.
b) Each individual B cell produces many different types of antibodies that can bind a range of
targets (epitopes).
c) Isolated B cells that produce a specific kind of antibody are fused with a type of cancer cell to
form a cell called a hybridoma.
d) To use antibodies to label a sample, a primary antibody that binds to a specific type of molecule
in the sample is used first.
e) Following binding of a primary antibody, a secondary antibody that is conjugated to fluorescent
dyes and that binds to the primary antibody is used.
b) Each individual B cell produces many different types of antibodies that can bind a range of
targets (epitopes).
Which of the following about resolution in microscopy is FALSE?
a) The resolution limit of a sample observed in red light (λ= 620 nm) with an objective lens with a
Numerical Aperture (NA) of 1.41 is better (lower) than a sample observed in green light (λ= 530
nm) with an NA of 1.27.
b) The resolution limit is the minimum distance between two objects so that the two objects can still
be distinguished as two objects in an image.
c) The resolution limit of a sample observed in blue light (λ= 486 nm) with an objective lens with a
Numerical Aperture (NA) of 1.41 is better (lower) than a sample observed in green light (λ= 530
nm) with an NA of 1.27.
d) The resolution limit of a sample observed in orange light (λ= 550 nm) with an objective lens with
a Numerical Aperture (NA) of 1.45 is better (lower) than a sample observed in green light (λ=
530 nm) with an NA of 1.25.
e) The resolution limit of light microscopy is the result of diffraction of light that is caused by
patterns of constructive and destructive interference of light waves as they pass near objects.
a) The resolution limit of a sample observed in red light (λ= 620 nm) with an objective lens with a
Numerical Aperture (NA) of 1.41 is better (lower) than a sample observed in green light (λ= 530
nm) with an NA of 1.27.
Green fluorescent protein (GFP)
a) can be used to identify the types of cell in which a specific gene is active (undergoes
transcription into mRNA and then translation into protein).
b) is a protein that was initially identified from tree frog eyes and is part of the photo-visual cortex
of these frogs that allows them to see at night.
c) is a type of quantum dot that relies on a semiconductor core to have fluorescent capabilities.
d) is a type of antibody that is used to detect the position of a specific type of protein in a sample
based on the interaction of GFP with a specific epitope (target).
e) is a type of secondary antibody that is used to detect the position of primary antibodies within a
biological sample.
a) can be used to identify the types of cell in which a specific gene is active (undergoes
transcription into mRNA and then translation into protein).
Fluorescence involves which of the following:
a) the emission of light of a higher (longer) wavelength than the excitation light absorbed by the
molecule.
b) formation of a new covalent bond upon absorbance of light, such that this covalent bond always
remains after the fluorescent light has been emitted.
c) the transition of an electron to a higher energy state upon excitation with light of a specific
wavelength, which rapidly results in emission of light of a smaller (lower) wavelength.
d) a reaction that has an overall net positive ΔG, when considering both the excitation and
emission phases of fluorescence
e) a molecule that absorbs a photon of light followed by non-radiative decay of the energy from that
electron leading only to the release of heat energy
a) the emission of light of a higher (longer) wavelength than the excitation light absorbed by the
molecule.
Some dyes are only fluorescent when they are found a specific type of chemical environment.
Which of the following can detect the presence of Calcium ions?
a) Green Fluorescent Protein
b) Red Fluorescent Protein
c) FM4-64
d) Calcein
e) Fura-2
e) Fura-2
Cholesterol
a) is an entirely non-polar (hydrophobic) molecule such that it is located entirely in the core of the
hydrophobic portion of a lipid bilayer.
b) has a specific structure that allows the presence of cholesterol in a lipid bilayer to decrease the
permeability of water.
c) has a rigid steroid ring structure, such that the presence of cholesterol decreases the packing
between other lipids in the lipid bilayer, making the membrane more fluid and loose.
d) is a type of glycerophospholipid.
e) has a phosphate headgroup that is the only region of this molecule that is polar
b) has a specific structure that allows the presence of cholesterol in a lipid bilayer to decrease the
permeability of water.
Which of the following about the lipids that make up a lipid bilayer is FALSE?
a) Glycerophospholipids such as phosphatidylethanolamine are amphipathic – they have both
polar and non-polar components.
b) Glycerophospholipids require an esterification reaction between fatty acids and the glycerol
backbone.
c) The fatty acid chains within the glycerophospholipids are the polar portion of these lipids.
d) Phosphatidylserine is unique among the other glycerophospholipids we discussed in that it is the
only one that has an overall net charge of -1 for its polar headgroup.
e) Sphingomyelin has some similarities to glycerophospholipids but is not a glycerophospholipid
and is synthesized inside cells in a different manner.
c) The fatty acid chains within the glycerophospholipids are the polar portion of these lipids.
Which of the following about the formation of lipid bilayers is TRUE?
a) Glycerophospholipids form lipid bilayers in which the polar headgroups are pushed to the
hydrophilic interior of the membrane and the non-polar acyl groups face the exterior or the
membrane.
b) Glycerophospholipids that have one acyl chain are just as likely to spontaneously form lipid
bilayers as glycerophospholipids with two acyl chains.
c) Glycerophospholipids will spontaneously form a lipid bilayer in an aqueous environment that will
remain stable as a flat membrane.
d) In water, lipid bilayers made up of glycerophospholipids with two acyl chains adopt a sphere like
structure called a liposome that has a water-filled (aqueous) interior.
e) Lipid bilayers is the name of Drake’s new album in which at least three songs are about where to
get the best deep-fried donuts in the Six.
d) In water, lipid bilayers made up of glycerophospholipids with two acyl chains adopt a sphere like
structure called a liposome that has a water-filled (aqueous) interior.
Provide a brief definition for each of the following:
(a) Lysosome
(b) Transcription
(c) Ribosomal RNA
(d) Anabolic reactions
(e) Lipid Bilayer
(A) A membrane bound organelle that is involved in the degradation (breakdown) of macromolecules
such as lipids.
(B) The process of creating an RNA molecule with a nucleotide sequence based on a the nucleotide
sequence of a corresponding segment of DNA.
(C) a type of RNA molecule that makes up the ribosome (not needed for full marks, but rRNA is the
catalytic core of the ribosome).
(D) Reactions that are endergonic (also acceptable: that decrease disorder and/or store energy in
bonds, also acceptable: reactions that lead to the synthesis of macromolecules)
(E) a biological membrane that is formed spontaneously by amphipathic molecules like
glycerophospholipids with a hydrophobic core and hydrophilic surface.
(A) Consider a chemical reaction that involves three molecules of substrates that combine to form one
molecule of product. The change in enthalpy (ΔH) for this reaction is positive. Is this a spontaneous
(favourable) or non-spontaneous (unfavourable) reaction? (6 marks).
Hint: Include in your answer how enthalpy and entropy contribute to the change in free energy of
a reaction. Also describe how these parameters tell you about the change in free energy in this
specific reaction.
(B) What is the phenomenon that allows some reactions that in isolation are non-spontaneous
(unfavourable) to nonetheless occur in the context of a living cell? Provide a brief explanation for this
phenomenon, and the most common “other” molecule involved in this in cells. (3 marks)
(A) Since the reaction involves three molecules of substrates being combined into one molecule of
product, this means that the reaction is more ordered or less disordered (1 mark). This means that the
reaction has a negative ΔS (1 mark, or negative change in entropy).
Gibbs free energy (ΔG) (1 mark) describes the overall change in free energy and is determined as
follows: ΔG = ΔH - TΔS (1 mark)
2
In this reaction, since ΔS is negative and ΔH is positive, the outcome is that ΔG is also positive (1
mark), so that this reaction is unfavourable (1 mark).
(B)
In a living cell, unfavourable reactions can be coupled to a favourable reaction (1 mark) which would
make the overall sum of these reactions when taken together to be favourable (1 mark).
The most common other molecule involved in this in cells is ATP (adenosine triphosphate) (1 mark).
Some proteins are regulated (controlled) by the covalent attachment of a phosphate group to that
protein, a process called phosphorylation. Let’s consider a protein X that undergoes phosphorylation
and becomes active when it is covalently bound to the phosphate.
(A) Describe the proteins involved in both adding and removing this phosphate group from Protein X,
and how this leads to control of the function of Protein X (4 marks).
Hint: Include in your answer the names of the other proteins involved and what each does to
protein X. Also consider how the specific properties of the phosphate attached to protein X may
impact the function of protein X.
(B) The specific amino acid that is modified covalently with the phosphate on Protein X is now replaced
with glutamate, an amino acid that cannot be covalently attached to a phosphate. Glutamate is an
amino acid with a large, negatively charged R group. Is this altered version of protein X likely to be
active or not?
(A)
- A Kinase is an enzyme that will attach the phosphate to protein X (1 mark)
- A phosphatase in an enzyme that will remove the phosphate from protein X (1 mark)
- A phosphate is a large, negatively charged chemical group (1 mark) that alters electrostatic
and polar interactions on protein X enough to change the function (1 mark).
(B)
- Despite not being able to be bound to a phosphate, the negatively charged glutamate may
have the same result as the covalent addition of phosphate group on the structure of the protein
(1 mark), thus this mutated version of protein X is likely to be active (1 mark).
(A) How does fluorescence recovery after photobleaching (FRAP) allow you to study the movement
(dynamics) of proteins inside a living cell? (4 marks)
Hint: Include in your answer the steps involved in this experiment and an explanation of how this
allows you to measure the movement of a particular protein.
FRAP begins with a cell that has a specific protein or other molecule labelled with a fluorescent dye (1
mark).
- a region of the cell is subjected to photobleaching by high intensity light, which leads to permanent
destruction of the dye molecules in that region (1 marks).
- the recovery of fluorescence in the bleached region can only come from the movement of
(unbleached) dye molecules from the regions of the sample that were not photobleached (1 mark).
- the rate of recovery of the fluorescence tell you about the rate of movement of molecules in that cell
sample (1 mark).
