Exam 2 Flashcards
What could be defined as an organized network of extracellular materials found beyond the immediate vicinity of the plasma membrane?
extracellular matrix
You place mammary gland epithelial cells in culture and then treat them with enzymes that digest the surrounding extracellular matrix. What happens?
the secretory and synthetic activities of the cells decrease
The basal lamina of which structure may thicken abnormally in long-term diabetics causing kidney failure?
the glomerulus
All collagen family members consist of __ chains arranged in a __
3, triple helix
Collagen fibrils are strengthened by covalent cross-links between __ and __ residues on adjacent collagen molecules
lysine, hydroxylysine
In the corneal stroma, the uniformity of collagen fiber size and the ordered packing of the fibers confers what property on the corneal stroma?
transparency
Basement membranes contain Type IV collagen, a non fibrillar collagen organized in a flattened network. The Type IV collagen trimer has some interspersed non helical segments. What property does this confer upon basement membranes?
flexibility
Type I collagen mutations cause a potentially lethal condition characterized by extremely fragile bones, think skin, and weak tendons. This condition is called
osteogenesis imperfecta
Type II collagen mutations alter the properties of cartilage tissue and are known to cause
dwarfism and skeletal deformities
Mutations in other collagen genes can lead to a variety of distinct but related defects in collagen matrix structure, one of which causes hyper flexible joints and highly extensible skin. These defects are usually referred to as
Ehler-Danlos syndromes
What substance joins proteoglycans together into gigantic complexes called proteoglycan aggregates? These complexes can occupy very large volumes
hyaluronic acid
If antibodies to fibronectin are exposed to an embryo through which neural crest cells are migrating, what happens?
neural crest cell movements are inhibited
What would be the effect on primordial germ cells when an embryo is exposed to laminin-specific antibodies?
their movement to the developing gonad is disrupted
The degradation of the extracellular matrix, along with cell surface proteins, is accomplished mostly by a __ -containing enzyme family called __
zinc, matrix metalloproteinases
What protein is thought to be secreted into the extracellular matrix that surrounds the lining of mature blood vessels, where it inhibits angiogenesis?
thrombospondin
What integral membrane protein family made of two membrane-spanning chains (a and b) is involved in attaching cells to their extracellular microenvironment?
integrins
In an integral, what structure is it that crosses the lipid bilayer?
a transmembrane helix
The activation of a membrane integrin by the binding of its cytoplasmic portion to molecules in the cytoplasm and the resultant increase in its affinity for an extracellular ligand is called
inside-out signaling
Evidence strongly suggests that the bent conformation of an integrin is __ and unable to bind its ligand
inactive
You are investigating the interactions of integrin a and b subunits and isolate the extracellular portion of an integrin as a soluble a/b heterodimer. The heterodimer lacks the associated transmembrane and cytoplasmic domains normally present as part of the molecule. You experimentally link the a and b subunits at the bases of their legs so that the ligand-binding regions of the a and b subunits approach one another. What is true about the molecules formed?
the molecules bind their ligand tightly
If experimentally linked a/b heterodimer integrin subunits are separated, what happens?
the molecules are unable to bind a ligand
What ion is not known to bind to integrins?
sodium
What kind of experiments have provided evidence that most interns have unique functions?
gene knockout experiments
You coat a Petri dish with fibronectin and proteoglycans and culture cells on the dish. The cells adhere to the dish. You repeat the experiment but this time add RGD tripeptides to the culture dish as the cells are added. What happens?
The cells do not adhere to the dish
You coat a Petri dish with fibronectin and proteoglycans and culture cells on the dish. The cells adhere to the dish. You repeat the experiment but this time add RGD tripeptides to the culture dish as the cells are added. The result of this experiment is an example of what biochemical process?
competitive inhibition
Why do cells flatten out as they make contact with a surface?
They send out projections that make increasingly stable attachments.
To what is the cytoplasmic domain of integrins in the region of a focal contact connected via various adaptors?
actin of the cytoskeleton
The tightest attachment between a cell and its extracellular matrix is seen at the site where an epithelial cell is attached to the underlying basement membrane. The specialized adhesive structure found at such a site is called a(n) ________.
hemidesmosome
Filaments connected to the dense plaque underlying the membrane in a hemidesmosome course outward into the cytoplasm. These filaments are composed of the protein _____ and are best known as ______.
keratin, intermediate filaments
Epidermolysis bullosa, an inherited blistering disease, is caused by
genetic alterations in any one of a number of hemidesmosomal proteins
Focal adhesions
collect information about the chemical properties of the extracellular environment
Which of the following proteins are known to be associated with focal adhesions?
actin and myosin
Cells were allowed to bind to beads that had been covered with a coating of fibronectin. When the membrane-bound beads were pulled by an optical tweezer, the resultant mechanical stimulus was transmitted into the cell interior. What response did this cause?
It generated a wave of Src kinase activity.
Mesenchymal stem cells were grown on a soft, pliable substratum. Into what type of cells did they develop?
nerve cells
Mesenchymal stem cells were grown on a substratum of moderate stiffness. Into what type of cells did they develop?
muscle cells
Mesenchymal stem cells were grown on a very stiff substrate. Into what type of cells did they develop
osteoblasts, which give rise to bone cells
The filaments associated with hemidesmosomes are
keratin filaments and intermediate filaments
In which disease do individuals produce antibodies that bind to proteins present in hemidesmosmes? It causes the lower layer of the epidermis to lose attachment to the underlying basement membrane and thus to the underlying connective tissue layer of the dermis. The leakage of fluid into the space beneath the epidermis results in severe blistering of the skin.
bullous pemphigoid
Which disease is an inherited blistering disease that can occur in patients with genetic alterations in any one of a number of hemidesmosomal proteins, including the α6 or β4 integrin subunit, collagen VII or laminin-5?
epidermolysis bullosa
What proteins have been shown to be altered by genetic mutations in patients who suffer from epidermolysis bullosa?
the α6 integrin subunit, the β4 integrin subunit, collagen VII, laminin-5
You disaggregate cells from two different developing organs and mix them together. Initially, they form a mixed clump. What happens next?
The cells sort themselves out so that each cell adhered only to cells of the same type
________ are members of an integral membrane glycoprotein family that bind to specific sugar arrangements in oligosaccharides that project from the surfaces of other cells.
Selectins
Lymphocytes are isolated and labeled with radioactive isotopes. They are then exposed to frozen tissue sections of a lymphoid organ. What happens?
The lymphocytes selectively adhere to the endothelial lining of venules in peripheral lymph nodes.
The binding of lymphocytes to the endothelial lining of venules in peripheral lymph node frozen tissue sections could be blocked in what way? This demonstrated the existence of what kind of molecule?
Treatment with antibodies against specific lymphocyte surface glycoproteins, selectins
While most IgSF members are involved in various aspects of immune function, some of them mediate ________ cell-cell adhesion
calcium-independent
The bonds that selectins form with their ligands become _______ when the interaction is __________
stronger, placed under mechanical stress
What is thought to be the origin of immunoglobulins?
They may be derived from cell-adhesion receptors in invertebrates.
What is the function of most IgSFs?
mediating specific interactions of lymphocytes with cells needed for the immune response
L1 is an IgSF molecule that has been shown to be important in neural development; it is thought that it may be involved in axon growth within the embryonic nervous system. What evidence supports this statement?
People who die of L1-deficiency are often missing two large nerve tract
Patients that have died of L1-deficiency disease are missing a nerve tract that ________.
1) runs between the brain and the spinal cord
2) runs between the two halves of the brain
3) runs between the spinal cord and cerebellum
4) runs between the brain and the endocrine system
1 and 2
You genetically engineer nonadhesive cells to express one variety of cadherins and then mix the cells in various combinations. You then monitor their interactions. What do you observe?
The genetically engineered cells adhered preferentially to cells expressing the same cadherins.
Cadherins appear to be important in holding cells together in __________ tissues.
tightly cohesive
Calcium ions form bridges between
successive domains of a given cadherin molecule
What determines the strength of adhesion between apposing cells held together by cadherins?
d) the number of cadherins in a cluster connecting the cells
57) The loss of cadherin function may be instrumental in what disease state?
c) the spread of malignant tumors
58) When tight junctions, gap junctions and desmosomes are arranged in a specific array, the assortment of surface specializations is called a(n) __________.
d) junctional complex
59) From the apical surface to the basal surface of an epithelial cell, what is the order of cell junctions observed in the junctional complex?
a) tight junction, belt desmosome, spot desmosomes, gap junctions
60) What type of cell adhesion molecule is associated with cells being held together by adherens junctions at the site of the junction?
e) cadherins
61) What can be described as a tightly adherent, polarized cell layer?
c) an epithelium
62) What can be described as solitary, nonadhesive, nonpolarized migratory cells?
a) a mesenchyme
63) Which of the following is typified by an epithelial-mesenchymal transition or EMT?
1) formation of the mesoderm during gastrulation in a chick or mammalian embryo
2) cells breaking away from a from a cohesive epiblast
3) fusion of sperm and egg
4) formation of cartilage
e) 1 and 2
64) Which of the following tissues are typically derived from mesenchymal cells?
e) mesodermal tissues, blood and muscle
65) Which of the following tissues are typically not derived from mesenchymal cells?
b) ectodermal tissues
66) The cells of the epiblast of a developing mammalian embryo display what cell adhesion molecules on their surfaces, molecules that presumably promote their close association with one another?
b) E-cadherins
67) What is thought to promote the release of future mesoderm cells from an epithelium and their transformation into mesenchymal cells?
a) a stoppage in the expression of E-cadherin genes
68) Which tissues below are typically derived from the single-celled epithelium on the dorsal surface of a chick embryo after gastrulation?
b) skin, ectodermal tissues and nervous system
69) Which tissues below are not typically derived from the single-celled epithelium on the dorsal surface of a chick embryo after gastrulation?
a) muscle
70) What changes in the central region of the dorsal surface of the single-celled epithelial layer of a chick embryo lead to the formation of the primitive nervous system?
1) a stoppage in the expression of E-cadherin genes
2) a stoppage in the expression of N-cadherin genes
3) an elevation in the expression of N-cadherin genes
d) 1 and 3
71) Which tissues below are typically derived from the cells on the dorsal surface of a mammalian embryo after gastrulation that express N-cadherins and stop expressing E-cadherins?
a) skin
b) only brain
c) only spinal cord
d) only neural tube
e) brain, spinal cord and neural tube
e) brain, spinal cord and neural tube
72) Which tissues below are not typically derived from the cells on the dorsal surface of a mammalian embryo after gastrulation that express N-cadherins and stop expressing E-cadherins?
a) skin
73) Cadherin clusters of adherens junctions _____________.
1) connect the external environment to the actin cytoskeleton
2) do not require calcium ions to perform their function
3) provide a pathway for signals to be transmitted from the cell exterior to the cytoplasm
4) connect the external environment to the vimentin cytoskeleton
e) 1 and 3
74) Desmosomes are particularly numerous in tissues _____________.
a) that are subjected to mechanical stress
b) like cardiac muscle
c) like the epithelial layers of the skin
d) like the epithelial layers of the uterine cervix
e) All of these are correct.
e
75) The cadherins of the desmosomes ____________.
1) have a different domain structure from classical cadherins
2) are referred to as desmogleins
3) are called desmocollins
d) 1, 2 and 3
76) Pemphigus vulgaris __________.
a) is characterized by a loss of epidermal cell-cell adhesion
b) is an autoimmune disease
c) is characterized by severe blistering of the skin
d) is caused by the production of antibodies against one of the desmoglzins
e. all are correct
e
77) Attachment of an integrin to its ligand can induce which of the following responses within a cell?
a) changes in cytoplasmic pH
b) changes in cytoplasmic C2+ ion concentration
c) protein phosphorylation
d) gene expression
e) All of these are correct.
e
78) Mammary gland epithelial cells are removed from a mammary gland and grown on a bare culture dish. What happens to them?
1) Nothing happens.
2) They lose their ability to synthesize milk proteins.
3) They appear as flattened, undifferentiated cells.
4) They become even more differentiated and proliferate at a high rate.
e) 2 and 3
79) When undifferentiated mammary gland epithelium cells that had been grown on a bare culture dish are cultured in the presence of certain extracellular molecules (e.g., laminin), what, if anything happens to them?
1) There is no change in these cells.
2) They regain their differentiated appearance.
3) They differentiate into muscle and bone cells.
4) They become organized into milk-producing, gland-like structures.
e) 2 and 4
80) Laminin is thought to stimulate mammary gland cells to differentiate into milk-producing gland-like structures. How does laminin accomplish this?
1) Laminin stimulates the mammary cells by binding to cell-surface integrins.
2) Laminin stimulates the mammary cells by binding to cell-surface selectins.
3) Laminin binding at the cell surface activates kinases at the inner surface of the membrane.
4) Laminin binding at the cell surface activates kinases on the membrane’s outer surface.
e) 1 and 4
81) What forms the barrier of the tight junctions that seals off the space between adjacent cells?
a) paired rows of aligned integral membrane proteins
82) Which tight junction will form a tighter seal?
a) one with a single strand of aligned integral membrane proteins
b) one with a number of parallel, interconnected strands of aligned integral membrane proteins
c) tight junctions containing a special kind of phospholipid
d) tight junctions containing a special kind of carbohydrate
e) one with a number of parallel, interconnected strands of interdigitated integral membrane
b
83) One small region of a human kidney tubule known as the thick ascending limb (or TAL) has tight junctions that are permeable to magnesium (Mg2+) ions. What is thought to account for the permeability of this tight junction to magnesium ions?
b) Loops of claudin molecules that extend into the extracellular space form pores in the TAL.
84) Animals lacking the claudin-1 gene suffered from ___________.
a) uncontrolled water loss
85) Despite the presence of the blood-brain barrier, what cells, oddly enough, can pass through the blood-brain barrier by sending a signal that opens up the junction?
b) immune system cells
86) The opening in the center of a connexon that allows the passage of solutes between cells is called a(n) ________.
b) annulus
87) Each connexon in a gap junction is constructed of ___ connexin subunits.
c) 6
88) During gap junction formation, connexons in apposing cells become tightly connected through extensive noncovalent interactions of __________.
b) connexin subunit extracellular domains
89) What kind of molecule does not pass through a gap junction?
d) ribosomes
90) A new type of communication system has been discovered that consists of thin, highly elongated tubules capable of conducting cell-surface proteins, cytoplasmic vesicles and calcium signals from one cell to another. This system is referred to as ________.
d) tunneling nanotubes
91) Which animal cell structure do plasmodesmata in plants most closely resemble?
d) gap junctions
92) What explains the fact that plants lack the specialized junctions seen in animal cells?
c) the presence of the cell wall
93) What lines the plasmodesmata?
d) the plasma membrane
94) The dense central structure that is derived from the smooth endoplasmic reticulum and usually seen in the plasmodesmata is called a(n) ________.
b) desmotubule
95) From what cell organelle does the desmotubule appear to be derived?
a) SER of the two cells
96) You are studying a plant and inject fluorescein, a fluorescent dye, into a single cell on the surface of the plant. After a brief period of time, the dye spreads to cells neighboring the injected cell. What do you conclude?
d) The cells are connected by plasmodesmata.
97) Which of the following is not a function of the plant cell wall?
a) It allows plant cells to develop osmotic turgor pressure that pushes against their surrounding walls.
b) It provides mechanical support for individual cells and serves as a type of “skeleton” for the whole plant.
c) It protects cells against damage from mechanical abrasion, osmotic influx of water & pathogens.
d) It prevents cell-cell interactions.
e) It can be a source of signals that alter activities of cells that it contacts.
d
98) The enzyme embedded in the plant cell membrane that catalyzes the growth of a cellulose molecule is called _________.
b) cellulose synthase
99) Which plant cell wall molecule is economically important as a component essential for the production of jams and jellies?
b) pectin
100) What class of plant cell proteins facilitates plant cell growth by causing a localized relaxation of the cell wall, which allows the cell to elongate at that site in response to turgor pressure generated within the cell?
c) expansins
101) What type of protein also seen in animal cells spans the plant plasma membrane and is thought to transmit signals from the cell wall to the cytoplasm?
a) protein kinase
102) Cell walls of young, undifferentiated plant cells must be able to grow along with the cells of which they are a part and thus exhibit extensibility. What are they known as?
a) primary walls
103) The thicker walls seen in mature plants that no longer allow extensive growth of the cell wall are known as _______.
b) secondary walls
104) How is the structure of the mature plant cell wall similar to the structure of the corneal stroma of the chicken embryo?
d) Both contain adjacent layers of fibers that are arranged perpendicular to each other.
1) Who was the first to report that certain rare inherited diseases were caused by the absence of specific enzymes?
b) Archibald Garrod
2) Alcaptonuria is a genetic disease that is characterized by _________.
a) urine turning dark upon exposure to the air
3) An alcaptonuric lacks the enzyme that oxidizes what metabolite?
c) homogentisic acid
4) What did Archibald Garrod call diseases like alcaptonuria?
e) inborn errors of metabolism
5) What did Beadle and Tatum use to generate mutations in their experimental organism?
b) irradiation with ultraviolet light
6) Beadle and Tatum’s research suggested that __________.
c) a gene carries the information for the construction of a particular enzyme
7) What was the new name of Beadle and Tatum’s hypothesis after it was discovered that some enzymes were composed of more than one polypeptide chain?
b) the One Gene – One Polypeptide hypothesis
8) Why has the One Gene – One Polypeptide hypothesis had to be modified?
b) Genes can be spliced differently to generate a variety of related polypeptides.
9) Which scientist is best known for his work on sickle cell anemia and proving the mechanism that causes the disease?
d) Vernon Ingram
10) What difference between sickle cell and normal hemoglobin is apparently responsible for all of the symptoms associated with sickle cell anemia?
a) The difference is a valine substitution in the mutant sickle cell hemoglobin for a glutamic acid in the normal molecule.
11) The enzyme in eukaryotes that is responsible for the synthesis of RNA from a DNA template is called _______.
b) DNA-dependent RNA polymerase
12) The site on DNA to which RNA polymerases bind before initiating transcription is called the ______.
promoter
13) What provides the energy that drives the polymerization of RNA from a DNA template?
c) ribonucleoside triphosphate precursors
14) The reverse reaction of nucleic acid synthesis almost never happens. What prevents it?
d) Nucleic acid synthesis is coupled to the highly exergonic pyrophosphate hydrolysis.
15) While RNA polymerase is a processive enzyme that remains attached to the DNA over long stretches of template, it must be associated _______ enough so that it can move from nucleotide to nucleotide along the template.
b) loosely
16) Once the σ factor leaves the core enzyme, what happens?
b) The core enzyme continues synthesis.
17) The nucleotide at which transcription is initiated is called _____.
b) +1
18) Sequences of DNA that are similar, seemingly conserved and seen in association with genes in roughly the same location from gene to gene in bacteria are called ________. They are generally the most common version of such a conserved DNA sequence, but some variation in the sequence can occur from one gene to another.
c) consensus sequences
19) The _______ is located about 10 bases upstream from the initiation site. It has the consensus sequence ______ and is responsible for identifying the precise nucleotide at which ________ begins.
a) Pribnow box, TATAAT, transcription
20) Once bound to the promoter, RNA polymerase ________.
b) melts the two DNA strands in the start site region
21) The corresponding segment of DNA from which the primary transcript is transcribed is called a _____.
b) transcription unit
22) What percentage of cellular RNA is rRNA?
c) more than 80%
23) What kind of DNA is the DNA that codes for rRNA?
b) moderately repetitive DNA
24) The chromosome regions containing rDNA are called ________.
b) nucleolar organizers
25) You are looking at an electron micrograph of several transcriptional units for rRNA. How can you tell where the transcription initiation site is?
c) It is near the shortest nascent transcripts.
26) The naked regions seen on the DNA fiber between transcriptional units are called ________.
b) nontranscribed spacers
27) A larger S value for an RNA specifically indicates that the RNA __________.
a) migrates more rapidly through a field of force during centrifugation
28) What features set pre-rRNAs apart from other RNA transcripts?
c) pseudouridine residues and methylated nucleotides
29) Modifications to the nucleotides of pre-rRNAs are made _________?
c) posttranscriptionally
30) Evidence of the importance of the conversion of uridine to pseudouridine comes from a rare, fatal disease in which the enzyme that catalyzes the conversion is mutated. Symptoms of the disease are skin abnormalities, bone marrow failure and elevated susceptibility to cancer. The name of the disease is _________.
dyskeratosis
31) In mammalian cells, radiolabeled methyl groups appear first in what size RNA molecule that is a precursor to rRNA?
a) 45S RNA
32) What is the name of the RNA-degrading machine that consists of nearly a dozen different exonucleases and is thought to execute some of the enzymatic cleavages that occur during pre-rRNA processing?
b) exosome
33) Where are the snoRNAs encoded?
d) within the intervening sequences of other genes
34) How would you describe the arrangement of the 5S rRNA genes?
a) tandem array with spacers
35) A cluster of genes coding for tRNAs is often referred to as ______.
a) tDNA
36) The promoter for tRNA genes (tDNA) is located ________.
b) within the coding section of the gene rather than in the 5’ flank
37) You incubate eukaryotic cells for 30 minutes in 3H-uridine and then immediately kill the cells and extract the RNA. Where does the radiolabel appear after this experiment?
a) in larger RNAs in the cytoplasm
38) Heterogeneous nuclear RNAs are _________.
b) mRNA precursors
39) Most of the cellular RNA is in what form?
d) rRNAs
40) How would you describe the half-lives of rRNAs and tRNAs?
a) days or weeks long
41) What is responsible for synthesizing hnRNAs?
b) RNA polymerase II
42) RNA polymerase II promoters are located on the ____ side of each transcription unit.
b) 5’
43) Why are general transcription factors (GTFs) referred to as “general?”
a) The same transcription factors are required for the accurate initiation of transcription of a diverse array of genes in a wide variety of different organisms.
44) What molecule is TFIIH known to phosphorylate?
b) RNA polymerase II
45) Where is the RNA polymerase II phosphorylated during its activation?
e) in the carboxyl-terminal domain (CTD) of the largest RNA polymerase II subunit
46) Which of the following is not a normal property of eukaryotic mRNAs?
b) They are found in the cytoplasm and inside the Golgi complex.
47) The 3’ end of most eukaryotic mRNAs contains a ______, while the 5’ end has a _________.
a) poly(A) tail, methylated guanosine cap
48) Which of the following binds to the TATA box?
d) TBP
49) The mRNA for which of the following proteins lacks a poly(A) tail?
d) histones
50) The intermediate stage that the group II introns pass through while undergoing self-splicing is called the _____.
c) lariat
51) The macromolecular complex that associates with each intron and splices it is called a(n) _____.
c) spliceosome
52) As life was first evolving, what molecule is thought to have performed double duty as the genetic material and performing catalysis of chemical reactions?
a) RNA
53) Which of the phenomena below is responsible for the ability of one gene to code for more than one polypeptide?
b) alternative splicing
54) The snoRNA genes are found in the ______ of genes coding for polypeptides involved in _______.
b) introns, ribosome assembly and function
55) A sense RNA for a particular targeted protein is ___________.
b) an RNA having the sequence of the mRNA that encoded the protein being targeted
56) RNA interference can be used to _____ the production of a particular enzyme so that the effect of the enzyme _______ on the organism’s _________ can be determined.
a) stop, deficiency, phenotype
57) RNAi or dsRNA-mediated RNA interference is an example of a broader phenomenon that occurs widely in eukaryotes called __________.
c) RNA silencing
58) Why does it make sense that cells would be able to recognize dsRNAs as undesirable using a mechanism such as RNAi?
a) dsRNAs are not produced by the cell’s normal genetic activities.
59) What is the name of the enzyme that cleaves dsRNA into the small, double-stranded fragments known as small-interfering RNAs (siRNAs)?
b) Dicer ribonuclease
60) What appears to be the role of siRNA in destroying the target mRNA upon which it and its associated proteins act?
d) It guides the RISC that cleaves the target mRNA to that target mRNA due to its complementarity to that molecule.
61) Which strand of the double-stranded siRNA is cut in two and then dissociates from the pre-RISC?
b) the passenger strand
62) How is the RISC directed to the target mRNA that it is destined to destroy?
b) The single-stranded siRNA is complementary to the target mRNA and directs the RISC to it.
63) It is generally accepted that vertebrates do not utilize RNAi as a defense against viruses for what reason?
1) Vertebrates have no serious viral infections.
2) Vertebrate cell membranes resist viral attachment.
3) Vertebrate cell walls resist viral attachment.
4) Vertebrates rely instead on a well-developed immune system.
d) 4
64) Mammalian oocytes have recently been shown to produce siRNAs. What are they called?
b) endo-siRNAs
65) What is the presumed function of the siRNAs produced by mammalian oocytes?
b) They may be the mechanism of defense against the movement of transposable elements in the female germ cell line.
66) A small RNA encoded by the lin-4 gene was found in the nematode C. elegans. It was nearly complementary to segments in ________. These small RNAs were able to bind to the complementary mRNA blocking its translation, which apparently triggers a transition to the next developmental stage.
a) the 3’ untranslated region of specific mRNAs produced by the organism
67) A pri-mRNA is cleaved within the nucleus by an enzyme called _______ into a shorter, double-stranded, hairpin-shaped precursor called a ________.
a) Drosha, pre-miRNA
68) Where is the pre-miRNA converted to miRNA by Dicer?
b) the cytoplasm
69) With what protein does the double-stranded miRNA become associated? The RNA duplex then is disassembled and one of the single strands is incorporated into a RISC complex.
c) an Argonaute protein
70) Which enzyme, also responsible for siRNA formation, carves miRNAs from their double-stranded, fold-back RNA precursor (pre-miRNA)?
c) Dicer ribonuclease
71) What are the differences between piRNAs on the one hand and si/miRNAs on the other hand?
a) piRNAs are longer than si/miRNAs.
b) The majority of mammalian piRNAs can be mapped to a small number of huge genomic loci, unlike si/mi RNAs.
c) The formation of piRNAs does not involve the formation of dsRNA precursors, unlike si/mi RNAs.
d) Formation of piRNAs does not involve cleavage by Dicer ribonuclease, but instead it depends on the endonuclease activity of the PIWI protein acting on a long, single stranded primary transcript.
e) All of these are correct.
e
72) You travel to another planet and discover that its genetic system is based on DNA, but it has 6 bases instead of 4 as happens on Earth. The proteins on the planet have 30 amino acids. What would be the likely number of letters in each codon on this planet?
b) 2
73) What evidence shows that the genetic code is not overlapping?
b) Mutant proteins whose genes experience a change in only one nucleotide, have a corresponding change in only 1 amino acid.
74) The genetic code has 64 codons, while there are only 20 amino acids. Thus, some amino acids are coded for by more than one codon. As a result, the genetic code is said to be ________.
b) degenerate
75) If there were one tRNA for every codon that codes for an amino acid, how many different tRNAs should there be?
d) 61
76) What is the maximum number of tRNAs that a cell would be likely to have?
d) 61
77) Before the genetic code was actually known, Francis Crick predicted that it was degenerate. What piece of evidence led him to make this prediction?
c) He noted that the base composition of the DNAs of various bacteria varied greatly while the amino acid composition of their proteins varied very little overall.
78) What is meant by referring to the genetic code as universal?
b) All of the organisms on Earth use the same genetic code with only minor variations.
79) Another name for protein synthesis is _________.
d) translation
80) Where are the unusual bases of tRNAs predominantly concentrated?
b) in the loops
81) What is the supposed function of the loops in tRNAs?
d) They serve as potential recognition sites for various proteins.
82) How do the unusual bases of the loops in tRNA influence tRNA structure?
a) They disrupt H bond formation in the loop regions causing the loops to form.
83) A tRNA has an anticodon with the sequence 3’-UAC-5’. What would be the sequence of the complementary codon? For the moment do not consider the wobble hypothesis.
c) 5’-AUG-3’
84) The greatest similarities among codons that specify the same amino acid occur _________.
a) in the first two nucleotides of the triplet
85) The greatest variability among codons that specify the same amino acid occurs _________.
d) in the third nucleotide of the triplet
86) What is the significance of the variability of the third nucleotide in a codon?
c) The same tRNA can recognize more than one codon.
87) Based on the interchangeability of the nucleotide at the third position, Francis Crick proposed that the same tRNA may be able to recognize more than one tRNA. What was his proposal called?
b) the wobble hypothesis
88) What enzyme is responsible for covalently linking amino acids to the 3’-end of the cognate tRNA?
b) aminoacyl-tRNA synthetase
89) Why does the isoleucyl-tRNA synthetase use two types of proofreading mechanisms to ensure its accurate aminoacylation?
c) Isoleucine is very hard to distinguish from valine, since they differ only by a single methylene group.
90) Which of the following is not required for protein synthesis?
d) anions
91) What are the three distinct activities of protein synthesis in the correct order?
a) initiation, elongation, termination
92) Which codon below usually serves as the initiation codon?
a) 5’-AUG-3’
93) What is the name of the nucleotide sequence that helps the 30S ribosomal subunit find the initiation codon on bacterial mRNAs?
d) the Shine-Dalgarno sequence
94) Which bacterial initiation factor facilitates attachment of the 30S subunit to the mRNA and may prevent the aminoacyl-tRNA from entering the wrong site on the ribosome?
b) IF1
95) What is always the first amino acid incorporated at the N-terminus of a nascent polypeptide chain?
c) methionine
96) What chemical group is attached to the first methionine in a polypeptide chain in prokaryotes?
a) a formyl group
97) The initiator tRNA enters the 30S ribosomal subunit at the ____ during prokaryotic protein synthesis.
b) P site
98) What is probably responsible for driving the conformational shift that is required for the release of the IF2-GDP initiation factor from the initiation complex?
b) hydrolysis of the GTP bound to IF2
99) The mechanical changes that ribosomes undergo are driven by energy from ______.
a) GTP hydrolysis
100) The surfaces of the two ribosomal subunits that face one another contain the binding sites for the mRNA and incoming tRNAs and are thus of key importance for the function of the ribosomes. The fact that these surfaces consist largely of RNA supports what proposal?
b) the proposal that primordial ribosomes were composed exclusively of RNA
101) It has been discovered that some mRNAs have a signal that causes the ribosome to change its reading frame by backing up or moving ahead one base. This can, in some cases, defend against a frameshift mutation. Such a sequence is called a(n) _________.
b) recoding signal
102) What amino acid is converted to selenocysteine after its attachment to its tRNA?
a) serine
103) In what direction is mRNA produced?
b) 5’ to 3’ direction
Which of the following words or phrases does not accurately describe the contents of the nucleus?
a) viscous
b) amorphous
c) undistinguished morphology
d) crystalline
e) highly extended nucleoprotein
d
2) Which of the following is not included within the nucleus of a typical interphase (nonmitotic) cell?
a) chromosomes
b) nuclear matrix
c) nucleolus
d) nucleoplasm
e) mesosome
e
3) What is probably the single most important distinction between prokaryotes and eukaryotes?
b) the separation of the cell’s genetic material from the surrounding cytoplasm
4) With what structure is the outer membrane of the nuclear envelope continuous?
a) RER
5) The thin filamentous meshwork within the nucleus that is bound by integral membrane proteins of the inner surface of the nuclear envelope in animal cells is called the _________.
c) nuclear lamina
6) What is the name of the proteins that make up the nuclear lamina and of what protein superfamily are they a member?
b) lamins, intermediate filaments
7) Which of the traits below is characteristic of the classical nuclear localization signals?
a) possession of large numbers of hydrophobic amino acids
b) possession of one or two short stretches of negatively charged amino acids
c) possession of one or two short stretches of positively charged amino acids
d) twisted backbones
e) double helical regions
c
8) A transport receptor that moves macromolecules from the cytoplasm to the nucleus is called a(n) ____.
c) importin
9) To what is the NLS – protein cargo – importing α/β complex thought to bind when it seems to dock to the outer surface of the nucleus near the nuclear pore complex?
d) cytoplasmic filaments that extend from the outer ring of the nuclear pore complex
10) What is used to maintain the Ran-GTP gradient across the nuclear envelope?
d) energy released by GTP hydrolysis
11) What happens if histone H1 is selectively extracted from compacted chromatin (30 nm fibers)?
a) 30-nm fibers uncoil to form a thinner, more extended beaded filament.
12) What experimental evidence suggests that the N-terminal tails of histones participate in the formation of higher-order chromatin structure?
c) Chromatin fibers prepared with H4 histones lacking their tails cannot fold into higher-order fibers.
13) The DNA loops of 80 – 100 nm fibers begin and end with _______.
a) AT-rich sequences
14) What is the name of the gene that makes the RNA thought to be responsible for the inactivation if the X chromosome?
b) XIST
15) What distinguishes the regulatory, noncoding RNA that is suspected of being responsible for X chromosome inactivation from other noncoding RNA molecules?
a) It is much larger than the other noncoding RNAs.
16) There are genes on the X chromosome that manage to escape inactivation by an as yet unknown mechanism. What particular genes are included in this group and what might be the reason that they remain activated?
b) genes that are also present on the Y chromosome; they will be expressed equally in both sexes
17) What evidence suggests that while the XIST gene may be required to initiate X chromosome inactivation, it may not be required to maintain it from one generation to another?
b) Some tumor cells in women contain inactivated X chromosomes whose XIST gene has been deleted.
18) What is thought to maintain X chromosome inactivation?
e) both repressive histone modifications and DNA methylation
19) What evidence suggests that RNAi plays a role in heterochromatization?
a) Deletion of RNAi components impair both methylation of histone H3K9 and heterochromatization.
20) What is the advantage of the highly condensed state of the DNA of mitotic chromosomes?
b) The highly condensed state favors delivery of an intact package of DNA to each daughter cell.
21) Scientists often stain chromosomes from mitotic cells and photograph the chromosomes in the microscope. Each chromosome is cut out of the photograph, the chromosomes are matched up in homologous pairs and they are placed in order of decreasing size. These pictures can be used to screen individuals for chromosomal abnormalities, like extra, missing or grossly altered chromosomes. What is such a picture called?
c) karyotype
22) An unusual stretch of repeated sequences at the tips of a DNA molecule forming a cap at each end of the chromosome is called a ________.
a) telomere
23) If cells cannot replicate the ends of their DNA, what should happen with each round of cell division?
d) The chromosomes should get shorter.
24) The fact that chromosomes should become shorter and shorter with each round of cell division is referred to as the ________.
e) the end-replication problem
25) In one rare disease, individuals suffer from bone marrow failure due to the inability of this blood-forming tissue to produce a sufficient number of blood cells over a human lifetime. What causes this condition?
1) Individuals have greatly elevated telomerase levels.
2) Individuals have greatly reduced telomerase levels.
3) Individuals are heterozygous for the gene that encodes the telomerase RNA.
4) Individuals are heterozygous for the gene that encodes the telomerase protein subunit.
e) 2, 3 and 4
26) Genes are physically moved to sites within the nucleus called _________, where the transcription machinery is concentrated and within which genes involved in the same response tend to become colocalized.
c) transcription factories
27) What is the name of the linkage than holds the lactose disaccharide together?
d) β-galactoside linkage
28) What two monosaccharides combine to form lactose?
b) glucose and galactose
29) A section of a bacterial chromosome in which genes for the enzymes of a particular metabolic pathway are clustered together in a functional complex under coordinate control is called a(n) ______.
b) operon
30) What is the name of the site where RNA polymerase binds to the DNA prior to the beginning of transcription?
c) the promoter
31) The operator __________.
a) is the site on the DNA where the repressor binds
32) What site on a bacterial operon segment of a chromosome is adjacent to or overlaps with a promoter?
a) operator
33) What is a regulatory protein for a gene? It binds to specific DNA sequences with high affinity and plays a predominant role in determining if a genome segment is transcribed or not.
d) the repressor
34) The lac operon is an example of a(n) _______ operon.
c) inducible
35) β-galactosidase is encoded by the ___________.
b) z gene of the lac operon
36) How do allolactose and lactose differ?
c) The type of linkage holding the two constituent sugars together differs between lactose and allolactose.
37) The type of control exercised if the interaction of a regulatory protein and DNA inhibits transcription.
b) negative control
38) Why was it initially expected that cloned animals might have a shorter life span?
a) The chromosomes of the donor nuclei had shortened telomeres.
39) Which of the following would be the most acceptable explanation for why cloned animals actually have telomeres of normal length on their chromosomes?
a) The telomeres were elongated before transfer to the egg by telomerase in egg cell cytoplasm.
b) The telomeres were elongated after transfer to the egg by telomerase in egg cell cytoplasm.
c) The telomeres were shortened before transfer to the egg by telomerase in egg cell cytoplasm.
d) The telomeres were shortened after transfer to the egg by telomerase in egg cell cytoplasm.
e) The telomeres were replaced prior to mitosis by DNA repair.
b
40) Which of the following is not a general description of the gene expression regulation mechanisms that operate in eukaryotic organisms?
a) transcriptional-level controls
b) processing-level controls
c) translational-level controls
d) replication-level controls
e) denaturation-level controls
d
41) Which level of control of gene expression is defined as determining if a particular gene can give rise to mRNA and, if so, how often?
a) transcriptional-level controls
42) What level of control of gene expression is defined as regulating whether or not a particular mRNA is actually used in protein synthesis and, if so, how long and for how long a period of time?
c) translational-level controls
43) The success of cloning experiments led to the conclusion that _________.
1) the transcriptional state of a differentiated cell is not irreversible
2) the transcriptional state chromatin in a differentiated cell is irreversible
3) the transcriptional state chromatin in a differentiated cell is not irreversible
4) a nucleus from a differentiated cell can be reprogrammed by factors residing in the cytoplasm of its new environment
e) 1, 3 and 4
44) During a cloning experiment, the nucleus of a differentiated cell ________.
1) is able to stop expressing the genes of the adult tissue from which it is taken
2) starts expressing the genes of the adult tissue from which it was taken after transplantation
3) begins to selectively express the genes that are appropriate for the activated egg in which it suddenly finds itself
4) begins to selectively express the genes that are appropriate for the adult tissue in which it suddenly finds itself
e) 1 and 3
45) You are interpreting data on a DNA chip or microarray. You expose the chip to a mixture of two cDNA populations: one from cells that were not treated with a glucocorticoid hormone (untreated controls; labeled with a red fluorescent dye) and a population from cells that were treated with glucocorticoid hormones (glucocorticoid-treated; labeled with green fluorescent dye). You look at a spot on the chip representing the gene for phosphofructokinase, a gene that is not affected by glucocorticoid treatment, but is instead expressed in all cells. What color should the spot representing the phosphofructokinase gene be?
c) yellow
46) You are interpreting data on a DNA chip or microarray. You expose the chip to a mixture of two cDNA populations: one from cells that were not treated with a glucocorticoid hormone (untreated controls; labeled with a red fluorescent dye) and a population from cells that were treated with glucocorticoid hormones (glucocorticoid-treated; labeled with green fluorescent dye). You look at a spot on the chip representing the gene for phosphoenolase, a gene that is turned off by glucocorticoid treatment, but is expressed in control, untreated cells. What color should the spot representing the phosphoenolase gene be?
a) red
47) Which type of molecule binds at the core promoter sites in association with RNA polymerase?
a) general transcription factors
48) The extent to which a given gene is transcribed presumably depends upon __________.
b) the particular combination of transcription factors bound to its upstream regulatory elements
49) You are working with adult mouse fibroblast cells. The genes for transcription factors from pluripotent stem cells are transduced into the adult fibroblast cells as part of viral vectors in various combinations, and once inside the cells they were expressed. What results were obtained?
1) The fibroblasts die.
2) A combination of transduced genes for only four specific transcription factors was sufficient to reprogram the fibroblasts into undifferentiated cells.
3) A combination of transduced genes for only four specific transcription factors was sufficient to cause the fibroblasts to behave like pluripotent ES cells.
4) A combination of transduced genes for only four specific transcription factors was sufficient to cause a terminal differentiation of the fibroblast cells.
e) 2 and 3
50) Which of the following is not a transcription factor identified as important for maintaining pluripotency in ES cells?
c) Cal
51) You are working with adult mouse fibroblast cells. The genes for transcription factors from pluripotent stem cells are transduced into the adult fibroblast cells as part of viral vectors in various combinations, and once inside the cells they were expressed. Cells are produced that are capable of dividing indefinitely in culture and of differentiating into all of the various types of the body’s cells. What are they called?
e) both iPS cells and induced pluripotent cells
52) Each transcription factor usually has at least two domains that mediate different aspects of their function. What are they?
a) the DNA-binding domain and the activation domain
53) What domain of a transcription factor is responsible for recognizing and associating with specific DNA base pair sequences?
a) the DNA-binding domain
54) Which transcription factor helps to activate genes needed for cell division?
a) Egr
55) The HLH motif is often preceded by a stretch of highly ______ amino acids whose ______ charged side chains contact DNA and determine the transcription factor’s sequence specificity.
a) basic, positively
56) What phenomenon greatly expands the diversity of regulatory factors that can be generated from a limited number of polypeptides?
a) heterodimerization
57) The combination of a basic stretch of amino acids and a leucine zipper is known as a(n) _____ motif.
b) bZip
58) The α-helical portions of the bZip proteins ______.
a) facilitate dimerization
59) The basic amino acid stretch in bZip proteins _______.
b) allows the protein to recognize a specific nucleotide sequence in DNA
60) Related proteins are often referred to as _________.
c) isoforms
61) When present, the TATA, CAAT and GC boxes are typically found within 100 – 150 bp upstream from the transcription start site. Due to their closeness to the start of gene, they are often called ______.
b) proximal promoter elements
62) You attempt deletion mapping of a part of the promoter region of a particular gene. You remove a short sequence of nucleotides. Once the altered DNA is transfected into cells, the cells are able to transcribe the transfected DNA in a normal fashion. What do you conclude?
c) The sequence that was removed is not an essential part of the promoter.
63) What strategy in transcription factor research allows the simultaneous monitoring of all sites in the genome that carry out a particular activity with the goal of identifying all of the sites bound by a given transcription factor under a given set of physiological conditions?
c) genome-wide location analysis
64) Treatment of fragmented DNA with a particular transcription factor attached at a number of sites with antibodies against that transcription factor will cause _________.
a) precipitation of DNA fragments bound to that transcription factor
65) When DNA-binding proteins are removed from immunoprecipitated DNA sequences and the DNA fragments precipitated by the antibody are subsequently sequenced directly to determine the genomic sites bound, the technique is called __________.
c) ChIP-seq
66) Transcription factors bound at the enhancer stimulate the initiation of transcription at the core promoter through the action of intermediaries called _____.
c) coactivators
67) Evidence suggests that _____ of ______ from nucleosomes in the wake of an elongating RNA polymerase prevents the inappropriate __________ within the internal coding region of a gene.
c) removal, acetyl groups, initiation of transcription
68) What evidence would suggest that histone acetylation provides a recognizable surface to recruit proteins that bind to acetylated histones?
a) Mutation of a lysine in the tail of histone H3 in a promoter region to an alanine, which cannot be acetylated, prevents the binding of transcription factors that normally bind to that promoter.
69) The enzymes that remove acetyl groups from histones in the chromatin are ________.
b) histone deacetylases
70) If an exon is not supposed to be included in the mature mRNA, it must be excised. With what other RNA sequences is it excised?
b) the flanking introns
71) Which genetic phenomenon below involves the conversion of specific nucleotides to other nucleotides after RNA has been transcribed?
c) mRNA editing
72 Messenger RNA editing is an example of gene expression at the _________ level.
d) posttranscriptional
73) When an adenine (A) is converted to an inosine (I), how is it subsequently read by the translational machinery?
1) It is read as a guanine (G).
2) It is read as a cytosine (C).
3) It is read as a uracil (U).
4) It is read as a thymine (T).
a) 1
74) What effect can mRNA editing have on a newly transcribed mRNA?
1) It can create new splice sites.
2) It can generate new start codons.
3) It can generate stop codons.
4) It can lead to amino acid substitutions.
e) 1, 3 and 4
75) In mRNA editing, to which nitrogenous bases is adenine converted by the enzymatic removal of an amino group?
b) inosine
76) What extends from the methylguanosine cap at the start of an mRNA to the AUG initiation codon?
c) the 5’ UTR
77) What extends from the termination codon at the end of an mRNA coding region to the end of the poly(A) tail?
d) the 3’ UTR
78) _______ mRNAs are preferentially localized at the anterior end of a fruit fly larva; ______ mRNAs are preferentially localized at the opposite or posterior end of the larva.
a) Bicoid, oskar
79) The oskar protein is required for the ________, which develop at the _______ end of the larva.
b) formation of germ cells, posterior
80) Why might localizing mRNAs in the oocyte be more efficient than localizing the proteins they encode?
c) Each mRNA can be translated into a large number of proteins.
272) The localization of mRNAs is mediated by specific proteins that recognize mRNA localization sequences on the mRNAs. What name has been given to these sequences?
c) zip-codes
81) What role are microfilaments thought to play in the localization of oskar and bicoid mRNAs in the fruit fly oocytes?
a) They are thought to anchor mRNAs in position after they have arrived at their destination.
82) Why does the activation of a protein kinase that acts on initiation factor eIF2 block protein synthesis?
b) Phosphorylated eIF2 cannot exchange its GDP for GTP, which is required for eIF2 to participate in another round of translation initiation.
83) Mechanisms have been discovered that regulate the rate of mRNA translation in response to changing cellular requirements; these mechanism can act at both the ______ and ______ levels.
c) global, specific
84) The inactive mRNAs that are stored in an egg prior to fertilization typically have ________.
c) shortened poly(A) tails
85) What is the normal length of a poly(A) tail?
c) about 200 adenosine residues
86) How short must the poly(A) tail get to cause the mRNA to be degraded rapidly?
d) about 30 adenosine residues
87) A complex of exonucleases that degrades mRNAs is called the ______.
c) exosome
88) Deadenylation, decapping and 5’ —> 3’ degradation occur within small, transient cytoplasmic granules called _________.
d) P-bodies
89) What may happen if a protein that is supposed to have a short survival time and that is involved in the initiation of cell division is not destroyed when it is supposed to be destroyed?
b) The cells may become malignant.
90) A specific internal sequence of amino acids that ensures that the protein containing it will not survive long within the cell is called a(n) _______.
b) degron
91) Covalent linkage to what small, highly-conserved protein marks proteins for destruction?
c) ubiquitin
92) What happens to membrane proteins that have been attached to a single ubiquitin molecule?
a) They are selectively incorporated into endocytic vesicles.
93) What kinds of proteins are usually recognized by the cap of a proteasome?
d) polyubiquitinated proteins
94) To which amino acid is the first ubiquitin on a polyubiquitinated protein attached?
e) lysine
