Developmental Biology Study Guide Questions
Course Introduction
Developmental Biology explores the processes by which organisms grow and develop, from fertilization to adult form. The course examines cellular differentiation, genetic regulation of development, pattern formation, morphogenesis, and the evolution of developmental mechanisms. Through the study of model organisms and experimental approaches, students gain insights into embryogenesis, organogenesis, regeneration, and congenital disorders. Emphasis is placed on molecular signaling pathways, gene expression, and the integration of cellular behaviors that shape the structure and function of living organisms across a diversity of species.
Recommended Textbook
Molecular Biology of the Cell 6th Edition by Bruce Alberts
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Chapter 1: Cells and Genomes
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Sample Questions
Q1) To trace family relationships between distantly related organisms such as humans, algae, bacteria, and archaea, one should compare their genomes in regions
A) that evolve rapidly.
B) that have a higher mutation rate.
C) that code for proteins.
D) where mutations are hardly tolerated.
E) where most mutations are selectively neutral.
Answer: D
Q2) All cells in a multicellular organism have normally developed from a single cell and share the same genome, but can nevertheless be wildly different in their shape and function. What in the eukaryotic genome is responsible for this cell-type diversity?
A) The genes that encode transcription regulatory proteins
B) The regulatory sequences that control the expression of genes
C) The genes that code for molecules involved in receiving cellular signals
D) The genes that code for molecules involved in sending cellular signals to other cells
E) All of the above
Answer: E
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3
Chapter 2: Cell Chemistry and Bioenergetics
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Sample Questions
Q1) A hydrophobic molecule is typically
A) able to form hydrogen bonds with itself but not with water.
B) able to form hydrogen bonds with water.
C) charged.
D) hard to dissolve in a solvent.
E) incapable of interacting favorably with water.
Answer: E
Q2) Indicate whether each of the following descriptions matches glycolysis (G) or the Krebs cycle (K). Your answer would be a four-letter string composed of letters G and K only, e.g. GGGK.
( ) It oxidizes acetyl CoA to CO?.
( ) In eukaryotic cells, it is carried out in the cytosol.
( ) It produces FADH?.
( ) ?-Ketoglutarate, one of its intermediates, is used to synthesize the amino acid glutamic acid.
Answer: K G
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Chapter 3: Proteins
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Sample Questions
Q1) The turnover number for an enzyme is equivalent to the number of substrate molecules processed per second per enzyme molecule. To a test tube containing a 100 mM concentration of its substrate, you have added an enzyme at a final concentration of 10 µM, and have measured the rate of the reaction to be approximately 500 µM/sec. If the Km for the binding of the enzyme to this substrate is about 100 mM, what is the turnover number?
A) 100
B) 500
C) 1000
D) 5000
E) 10,000
Answer: A
Q2) Some protein domains are found in many different proteins and have been especially mobile during evolution. A domain of this kind is called a "protein "
Answer: module
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Chapter 4: DNA, Chromosomes, and Genomes
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Q1) In each of the following comparisons, indicate whether the molecular clock is expected to tick faster on average in the first (1) or the second (2) case. Your answer would be a four-digit number composed of digits 1 and 2 only, e.g. 2222.
( ) 1: The exons, or 2: the introns of a gene
( ) 1: The mitochondrial, or 2: the nuclear DNA of vertebrates
( ) 1: The first, or 2: the third position in synonymous codons
( ) 1: A gene, or 2: its pseudogene counterpart
Q2) A DNA nucleotide pair has an average mass of approximately 660 daltons. Knowing the number of nucleotides in the human genome, how many picograms of DNA are there in a diploid human nucleus? Avogadro's number is 6 × 10²³. Write down the picogram amount without decimals (round the number to the closest integer), e.g. 23 pg.
Q3) If species A in the distance matrix represents human, indicate which of the other species (B to D) represents chimpanzee, gorilla, and orangutan, respectively. Your answer would be a three-letter string composed of letters B, C, and D only, e.g. DCB.
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Chapter 5: DNA Replication, Repair, and Recombination
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Q1) Which of the following is NOT correct regarding long and short interspersed nuclear elements?
A) Each of them encodes a reverse transcriptase.
B) They rely on the cellular transcription machinery to produce their RNA transcript.
C) They use one of the strands in the target DNA as a primer to synthesize their DNA.
D) Together, they make up about 40% of our genome.
E) They can move into new regions of genome that do not have any homology with their DNA.
Q2) Which of the following is true regarding retroviral-like retrotransposons?
A) They encode both a reverse transcriptase and an RNA polymerase.
B) They have directly repeated long terminal repeats at their two ends when integrated into chromosomal DNA.
C) Their genomic RNA can be translated to produce viral coat proteins.
D) They leave double-strand breaks in the original donor DNA.
E) The Alu element in our genome is an example of retroviral-like retrotransposons.
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Chapter 6: How Cells Read the Genome: From DNA to Protein
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Q1) Eukaryotic pre-mRNAs undergo a number of modifications such as capping at the 5' end. A 5' cap...
A) consists of a modified terminal adenine nucleotide.
B) has a 3'-to-5' linkage between the terminal nucleotide and the 5' end of the pre-mRNA.
C) contains a triphosphate bridge between the terminal base and the 5' end of the pre-mRNA.
D) carries a negative charge in the terminal base due to methylation.
E) is identical for all mRNAs that are transcribed by RNA polymerase II.
Q2) Cajal bodies in the eukaryotic cell nucleus...
A) are stockpiles of fully mature snRNPs and other RNA processing components.
B) can only be observed by electron microscopy.
C) are absolutely required in all cell types.
D) speed up the maturation and assembly of snRNPs and snoRNPs.
E) are the main sites of pre-mRNA splicing.
Q3) Fill in the blank. These RNA molecules can catalyze a wide variety of biochemical reactions, including peptide bond formation and RNA splicing. They can be found in nature or selected in vitro for a desired function. Such a molecule is called a(n) ...
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Chapter 7: Control of Gene Expression
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Sample Questions
Q1) Indicate true (T) and false (F) statements below regarding P-bodies. Your answer would be a four-letter string composed of letters T and F only, e.g. TTFT.
( ) P-bodies are membrane-enclosed organelles scattered throughout the cytoplasm.
( ) mRNAs that are to be degraded are transferred from P-bodies to stress granules containing decapping and exonuclease enzymes.
( ) When translation initiation is blocked, stress granules typically shrink.
( ) mRNAs associated with stress granules are primed for translation.
Q2) Comparing the bacterial CRISPR system and the eukaryotic RNAi mediated by siRNAs, indicate whether each of the following CRISPR components is most analogous to Argonaute (A), siRNA (S), or target mRNA (T) in the RNAi pathway. Your answer would be a three-letter string composed of letter A, S, and T only.
( ) Cas
( ) Viral DNA
( ) crRNA
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Page 9
Chapter 8: Analyzing Cells, Molecules, and Systems
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Q1) Sort the following cellular components to reflect the centrifugal force required to sediment them by preparative ultracentrifugation, from low to high force required. Your answer would be a four-letter string composed of letters R, M, L, and N, e.g. LRNM. (L) Lysosomes
(M) Microsomes
(N) Nuclei
(R) Ribosomes (free cytosolic)
Q2) Indicate whether each of the following descriptions better applies to cDNA libraries (C) or genomic DNA libraries (G). Your answer would be a five-letter string composed of letters C and G only, e.g. CGCGC.
( ) Their production requires use of reverse transcriptase. ( ) They are enriched in protein-coding genes.
( ) Different sequences are represented in them based on their transcription level.
( ) They contain intronic sequences.
( ) They are cell-type specific.
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Chapter 9: Visualizing Cells
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Q1) Consider an engineered chimeric protein made from fusion of three proteins: a blue fluorescent protein (BFP), a calmodulin-binding peptide, and a green fluorescent protein (GFP). Calmodulin is an abundant calcium-binding protein in eukaryotes. Once bound to calcium ions, it can recognize the calmodulin-binding peptide in the fusion protein, change conformation, wrap around the peptide, and bring the BFP and GFP components in close proximity. This results in fluorescence resonance energy transfer (FRET) between BFP and GFP. Accordingly, the fusion protein
A) is a luminescent ion-sensitive indicator that red-shifts its emission wavelength in the presence of calcium.
B) is a luminescent ion-sensitive indicator that increases its emission in the presence of calcium.
C) is a genetically encoded calcium indicator that red-shifts its emission wavelength in the presence of calcium.
D) is a genetically encoded calcium indicator that increases its emission in the presence of calcium.
Q2) According to the force-extension graph, how many immunoglobulin domains are unfolded in each of these experiments? Write down the number as your answer, e.g. 9.
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Chapter 10: Membrane Structure
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Sample Questions
Q1) Under certain conditions, about 20 molecules, on average, are predicted to exist in each -octylglucoside detergent micelle. If the critical micelle concentration for this detergent is about 20 mM under these conditions, at what total -octylglucoside concentration are about half of the detergent molecules found in micelles?
A) 1 mM
B) 10 mM
C) 20 mM
D) 21 mM
E) 40 mM
Q2) While examining the crystal structure of a membrane protein, you find several phospholipid molecules bound to the protein. You know that these lipids
A) are thought to help stabilize many membrane proteins.
B) may enhance the crystallization of the bound membrane proteins.
C) interact specifically with the protein.
D) can have head groups of various sizes and charges depending on the protein.
E) All of the above.
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Chapter 11: Membrane Transport of Small Molecules and the Electrical Properties of Membranes
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Q1) The nicotinic acetylcholine receptor is an ionotropic receptor that can be activated by nicotine, a stimulant drug found in cigarettes. Additionally, ?-bungarotoxin, a neurotoxin found in the venom of some snakes, binds preferentially and tightly to the closed conformation of the receptors. Another drug, donepezil, is a potent acetylcholinesterase inhibitor used to treat patients with Alzheimer's disease. If applied at a neuromuscular junction, indicate whether each of the compounds (1) acetylcholine, (2) nicotine, (3) ?-bungarotoxin, and (4) donepezil would enhance (E) or suppress (S) the Ca<sup>2+</sup>influx in the muscle cells. Your answer would be a four-letter string composed of letters E and S only, e.g. EESS.
Q2) From left to right, indicate whether the transmitter-gated channels for (1) calcium, (2) chloride, (3) potassium, and (4) sodium at a chemical synapse usually open in response to excitatory (E) or inhibitory (I) neurotransmitters. Your answer would be a four-letter string composed of letters E and I only, e.g. EEIE.
Q3) Each single neuron acts as a computational device. Typically, the magnitude of the combined postsynaptic potential is encoded in the ... of firing of action potentials in the postsynaptic neuron.
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Chapter 12: Intracellular Compartments and Protein Sorting
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Q1) Rough microsomes can be subjected to a "salt extraction" procedure in which a high salt concentration is used to remove membrane-associated ribosomes and peripheral proteins. Such salt-extracted microsomes are known to be translocation-incompetent, meaning that when present co-translationally in vitro, they fail to protect translated proteins from protease digestion. However, adding back an 11S particle (S is the sedimentation coefficient) purified from the salt-wash fraction is sufficient to restore the protein-translocation activity of the salt-extracted microsomes. Which of the following do you think is true regarding the 11S particle?
A) It is composed of 21 proteins.
B) It is a digestion product of ER-associated ribosomes.
C) It is normally assembled in the nucleus and exported to the cytoplasm by exportins.
D) It is an ER integral membrane protein that can interact with the translocon.
E) It requires high salt concentration for its function in vivo.
Q2) Consider two cells, A and B. Both are approximately spherical, but cell A is a bacterium with a diameter of only about 1 µm, while the diameter of the eukaryotic cell B is about 10 µm. If the plasma membrane in the eukaryotic cell comprises only about 2% of the total cell membrane, which cell has a higher ratio of total cell membrane to volume? Write down A or B as your answer.
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Chapter 13: Intracellular Membrane Traffic
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Q1) An animal cell has been wounded and has a small rupture in its plasma membrane. Which of the following is more likely to happen next?
A) The cell rapidly cleaves by cytokinesis.
B) The rate of receptor-mediated endocytosis is increased.
C) The rate of exocytosis is increased.
D) The rate of pinocytosis is increased.
E) All of the above.
Q2) You have engineered a fusion protein composed of a cis Golgi resident protein and the green fluorescent protein. Similarly, you have made a fusion protein composed of a trans Golgi protein and the red fluorescent protein. You express these proteins in cells and follow individual Golgi cisternae using fluorescence microscopy. You observe that each individual cisterna emits a green, faint yellow, or red fluorescent signal at different times: it initially shows green fluorescence, but the green fluorescent signal fades away with time, and instead red fluorescence appears in the same cisterna. Additionally, you do not observe any red fluorescent cisterna that becomes green over time. Do these observations agree better with the cisternal maturation model (C) or the vesicle transport model (V) for the organization of Golgi stacks? Write down C or V as your answer.
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Chapter 14: Energy Conversion: Mitochondria and Chloroplasts
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Q1) What is the main reason why atmospheric oxygen levels did not rise immediately after the mass production of the gas by photosynthetic bacteria?
A) Because oxygen was rapidly consumed by aerobic microorganisms.
B) Because oxygen was dissolved in water.
C) Because large amounts of ferrous ions reduced the oxygen molecules.
D) Because oxygen was rapidly recycled by early photosynthetic bacteria.
Q2) The electrons used in carbon fixation by chloroplasts ultimately come from
A) Atmospheric oxygen
B) Atmospheric carbon dioxide
C) Water
D) Glyceraldehyde 3-phosphate
Q3) Indicate whether each of the following descriptions better applies to photosystem I (1) or photosystem II (2). Your answer would be a four-digit number composed of digits 1 and 2 only, e.g. 2212.
( ) It reduces plastoquinone.
( ) It uses a manganese cluster to oxidize water.
( ) It is confined to unstacked thylakoids.
( ) It contains the special pair P???.
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Chapter 15: Cell Signaling
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Q1) Which of the following is a major consequence of activation of phospholipase C(PLC ) by the Gq trimeric GTPase?
A) Elevation of intracellular cAMP levels, leading to the activation of protein kinase A
B) Elevation of PIP levels in the plasma membrane, leading to the activation of protein kinase B
C) Elevation of intracellular Ca² levels, leading to the activation of protein kinase C
D) Elevation of IP in the plasma membrane, leading to the activation of protein kinase D
E) Elevation of intracellular cGMP levels, leading to the activation of protein kinase G
Q2) What is the major way by which the monomeric G protein Ras is activated in receptor tyrosine kinase signaling?
A) Activation of Ras-GAP
B) Activation of Ras-GEF
C) Inactivation of Ras-GAP
D) Inactivation of Ras-GEF
E) Inactivation of Ras-GDI
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Chapter 16: The Cytoskeleton
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Q1) The pathogen Listeria monocytogenes can hijack the actin cytoskeleton in human cells and spread inside the host. Indicate true (T) and false (F) statements below about this phenomenon. Your answer would be a four-letter string composed of letters T and F only; e.g. TTFF.
( ) The movement can be reconstituted in vitro by placing the bacteria in a mixture of actin, formin, gelsolin, and capping protein.
( ) Cofilin counteracts the movement by depolymerizing actin filaments.
( ) The actin filaments grow with their minus ends pointed toward the bacterium.
( ) The movement depends on myosin activity to transport the bacteria on the actin filaments.
Q2) The -tubulin ring complex is to microtubules what is to actin filaments.
A) the Arp 2/3 complex
B) the dynactin complex
C) the troponin complex
D) formin
E) contractile ring
Q3) Fill in the blank: Each microtubule is typically made of thirteen parallel . that associate laterally to form a hollow tube.
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Chapter 17: The Cell Cycle
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Q1) In a multicellular organism such as a mammal, loss-of-function mutations in many genes can contribute to the development of cancer. These genes are therefore called tumor suppressors. In their absence, the cell fails to stop progression through the cell cycle under conditions in which normal cells would arrest, paving the way for tumorigenesis. Indicate whether each of the following proteins is (Y) or is not (N) expected to be the product of a tumor suppressor gene based on its function in the cell cycle. Your answer would be a four-letter string composed of letters Y and N only, e.g. YNNN.
( ) Rb
( ) Myc
( ) p53
( ) p21
Q2) Which of the following events occurs at the onset of S phase in a mitogen-stimulated vertebrate cell?
A) Activation of Cdh1-APC/C
B) Activation of Rb
C) Activation of geminin
D) Activation of Cdc20
E) All of the above
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Page 19
Chapter 18: Cell Death
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Q1) Indicate true (T) and false (F) statements below regarding apoptosis in disease. Your answer would be a four-letter string composed of letters T and F only, e.g. TTTF.
( ) Either excessive or insufficient apoptosis can contribute to disease.
( ) Excessive apoptosis, in many cases, leads to autoimmune disease and cancer.
( ) In about half of human cancers, the tumor suppressor protein p53 is mutated.
( ) Drugs that interfere with the function of Bcl2 family proteins such as Bax and Bak may treat cancers by stimulating apoptosis.
Q2) Which of the following proteins activates the mitochondrial pathway of apoptosis?
A) The tumor suppressor protein p53, when activated in response to extensive DNA damage.
B) The BH3-only protein Bid, when cleaved by the initiator caspase-8 (from the extrinsic pathway).
C) The anti-IAP protein Omi, when activated by dephosphorylation.
D) The BH3-only protein Bad, when activated by dephosphorylation.
E) All of the above.
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Chapter 19: Cell Junctions and the Extracellular Matrix
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Q1) Plasmodesmata in plant cells are functionally similar to animal cells'
A) adherens junctions.
B) desmosomes.
C) gap junctions.
D) hemidesmosomes.
E) tight junctions.
Q2) Which of the following molecules is capable of tension-sensing by exposing binding sites for other proteins when mechanically stretched?
A) -Catenin
B) Talin
C) Fibronectin
D) All of the above
Q3) Type IV collagen molecules can interact at their C-termini to form dimers and at their N-termini to form tetramers. What category do you think this type of collagen belongs to?
A) Fibrillar
B) Fibril-associated
C) Network-forming
D) Proteoglycan core
E) Anchorage fibril
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Chapter 20: Cancer
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Q1) Indicate true (T) and false (F) statements below regarding the mutational landscape of cancer cells. Your answer would be a four-letter string composed of letters T and F only, e.g. TFFF.
( ) In each cancer, usually there is one driver mutation and a large number of passenger mutations.
( ) It is estimated that about 20% of our genes are cancer-critical.
( ) Cancer-critical genes can encode metabolic enzymes or components of the RNA splicing machinery.
( ) The karyotype is often severely disordered in cancer cells.
Q2) For each of the following genes involved in regulation of cell growth through the mTOR pathway, indicate whether the gene is activated (A) or inactivated (I) in cancer cells compared to normal healthy cells. Your answer would be a four-letter string composed of letters A and I only, e.g. AAAA.
( ) mTOR
( ) Akt
( ) PTEN
( ) PI3K
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Chapter 21: Development of Multicellular Organisms
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Q1) Cactus is a maternal-effect gene coding for an inhibitory protein in the Drosophila Toll signaling pathway that binds to Dorsal in the cytosol and keeps it from nuclear entry. Would you expect maternal loss-of-function mutations in Cactus to give rise to dorsalized or ventralized embryos? What about loss-of-function mutations in Decapentaplegic (Dpp)?
A) Dorsalized; dorsalized
B) Dorsalized; ventralized
C) Ventralized; dorsalized
D) Ventralized; ventralized
Q2) Mutations in certain components of the cell-cycle machinery in Drosophila melanogaster can be used to slow down the rate of progression through the cell cycle in the wing imaginal discs of the fly larvae, without a major effect on the rate of cell growth.
As a result, compared to wild-type flies, the wing in the mutant flies would
A) have a larger size (area) with a higher number of relatively normal cells.
B) have the same size, but with a higher number of relatively smaller cells.
C) have the same size, but with a smaller number of relatively larger cells.
D) have a smaller size with the same number of relatively smaller cells.
E) have a smaller size with a smaller number of relatively normal cells.
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Chapter 22: Stem Cells and Tissue Renewal
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Q1) Although quite inefficient, cloning by nuclear transplantation can be successful, as exemplified by cloning of the famous Dolly. Such a success implies that
A) nuclei can be reprogrammed by cytoplasmic factors in a foreign cytoplasm.
B) epigenetic changes in somatic cells are not functionally irreversible.
C) even a differentiated nucleus contains a complete genome, capable of supporting the development of an entire organism.
D) All of the above.
Q2) Cells of the inner cell mass in an early mammalian embryo can be isolated and grown in culture. Which of the following is NOT true regarding these cells?
A) They are totipotent.
B) They can be introduced into another developing embryo where their progeny become incorporated into the resulting adult animal, even into its germ line.
C) They are stem cells.
D) They can be manipulated in culture to give rise to almost any type of differentiated cell.
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Chapter 23: Pathogens and Infection
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Q1) Mycobacterium tuberculosis can cause tuberculosis, a life-threatening lung infection, but can also infect an individual asymptomatically for years. It is not considered to be part of the normal flora, and can infect healthy individuals upon exposure. It can only replicate in the host and thus mainly spreads by direct human contact. Mycobacterium tuberculosis is therefore
A) a facultative primary pathogen.
B) a facultative opportunistic pathogen.
C) an obligate primary pathogen.
D) an obligate opportunistic pathogen.
Q2) How does Helicobacter pylori persist in the hostile environment of the stomach?
A) By expressing adhesin proteins that bind to molecules on the surface of gastric epithelial cells
B) By producing the enzyme urease, which locally neutralizes the gastric acid
C) By chemotaxis, using flagella, toward gastric epithelial cells
D) By producing toxins that target both epithelial cells and immune cells
E) All of the above
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Chapter 24: The Innate and Adaptive Immune Systems
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Q1) Indicate true (T) and false (F) statements below regarding lymphocytes in the adaptive immune system. Your answer would be a four-letter string composed of letters T and F only, e.g. TTFF.
( ) To induce an adaptive immune response, an invading pathogen must invade a peripheral lymphoid organ.
( ) Lymphocytes continuously circulate between central and peripheral lymphoid organs.
( ) Upon encountering its specific antigen in a peripheral lymphoid organ, a lymphocyte remains there to proliferate and differentiate into effector and memory cells.
( ) Memory B and T cells do not recirculate, but rather remain in the peripheral lymphoid organ in which they develop.
Q2) Normally, naïve cytotoxic and helper T cells interact for the first time with foreign antigens presented by dendritic cells in
A) the thymus.
B) the bloodstream.
C) peripheral lymphoid organs.
D) the bone marrow.
E) inflamed tissues.
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