Ch. 10: The Nucleus Online Quiz (Essay) Flashcards
How does the clustering and transcriptional pattern for eukaryotic ribosomal RNA genes ensure that there will be equal numbers of copies of the major RNAs available for ribosome assembly?
Ribosomal genes are organized in tandem repeats that contain ___ ___ ___ of the 18S, 5.8S, and 28S rRNA sequence as a single gene unit. The transcript contains all three sequences, and hence, each is produced after processing of the pre-rRNA in the same amount. All this is located in the nucleolus. Transcription of 5S rRNA occurs outside the nucleolus and may not be as tightly linked in terms of amount.
one copy each
Ribosomal RNAs are methylated at specific nucleotide positions. To what extent is the specificity of nucleotide modification achieved through enzyme recognition of sequence and/or other mechanisms?
The sequence specificity of what is modified comes about through guide RNAs, ___, directing modifications. ___ are part of protein complexes. In the end, it is a protein that catalyzes the reaction.
snoRNAs (small nucleolar RNAs)
The nuclear localization signal (NLS) is not removed (cleaved off) after entry of the protein into the nucleus. In contrast, the targeting sequences of proteins destined for organelles such as the mitochondria are located at the N-terminus of the protein and cleaved off once the proteins reach the lumen of the organelle. What are two likely reasons that the nuclear localization signal (NLS) is not cleaved off for nuclear proteins?
During mitosis, the nuclear envelope disintegrates and the nuclear proteins are released into the cytoplasm. Once the envelope re-forms around the daughter nuclei, the nuclear proteins need to be ___ in, thus explaining the need for retention of the NLS. A second reason is that nuclear localization signals are ___ to the polypeptide. Cleaved targeting sequences are typically located at the N-terminus of the protein. Cleavage of an internal sequence has much more consequence for the overall structure of the protein than removal of an N-terminal sequence. In addition, many nuclear proteins ___ in and out of the nucleus, which would be a third reason for retaining the NLS.
retransported, internal, shuttle
What are the expected phenotypic consequences of a mutation in Ran GAP that reduces its affinity for cytoplasmic filaments of the nuclear pore?
Ran is important to both protein import into and export out of the nucleus. As part of importin recycling to the cytoplasm, Ran in the GTP-bound form complexes with importin inside the nucleus. Formation of this complex results in the release of importin from cargo and the importin/Ran-GTP complex is then recycled back to the cytoplasm. During nuclear protein export in general, GTP-bound Ran binds to exportin inside the nucleus to give rise to a Ran-GFP/exportin/cargo complex that is exported as a unit through the nuclear pore into the cytoplasm. In either case, Ran functions as a GTP-dependent molecular switch. Ran GAP bound to the cytoplasmic filaments of the nuclear pore complex activates the GTPase activity of Ran in the cytoplasm and bound GTP is cleaved to GDP. If Ran GAP were not bound to the cytoplasmic filaments, its effective local concentration would be ___, and the efficiency of Ran activation would be low. Low affinity would cause a distinct decrease in the Ran GTP gradient across the nuclear pore. This would reduce the efficiency of both import into the nucleus, which is dependent on importin recycling, and export from the nucleus. Phenotypically, cell growth rates would ___ and the defect might be so severe as to be lethal.
diluted, slow
What attributes of where replication and transcription occur within the nucleus leads to these sites being designated as “factories”?
DNA replication and its transcription into RNA occur within clustered regions of the nucleus where large complexes of ___ involved in the particular process are concentrated.
proteins
What is the role of nucleotide sequence in mediating the export of ribosomal RNA from the nucleus?
The recognized export sequences reside on the ___ associated with the ribosomal RNA rather than on the ribosomal RNA itself. For example, a specific exportin, Crm1, recognizes protein sequence features (i.e., amino acids) of proteins bound to the ribosomal RNA rather than the nucleotide sequence of the ribosomal RNA itself.
proteins (polypeptides being made)
In order to determine a chromosome’s distribution within the mammalian nucleus, probes were hybridized to repeated sequences rather than to a single gene. Why?
When tandemly arrayed, the repeated sequence gives a locally amplified signal. Hybridizing a nucleotide probe to a single gene on a chromosome would give the equivalent of a point signal for the chromosome. Chromosomes have many genes. Moreover, repeated sequences are spread across a given chromosome. Therefore, hybridizing a probe to a repeated sequence lights up the ___ ___.
whole chromosome
In many organisms, the nuclear envelope breaks down during mitosis. As part of this breakdown, the nuclear lamina that underlies the nuclear envelope breaks down. In fact, many investigators think that the breakdown of the lamina initiates envelope breakdown. Propose a reversible mechanism for controlling the polymerization state of the proteins that make up the nuclear lamina.
Reversible ___/___ would provide a mechanism for regulating the polymerization of nuclear lamins. When phosphorylated, negative charge repulsion would lead to dissociation, and after dephosphorylation repolymerization would occur.
Reversible phosphorylation/dephoshorylation
The activity of transcription factors is frequently regulated by means of their localization within eukaryotic cells, such that only upon stimulation is the transcription factor transported into the nucleus, where it can activate its target genes. For a transcription factor that has a nuclear localization signal (NLS), explain two mechanisms by which regulated transport can occur.
Two possible mechanisms involve the masking the NLS such that it is not recognized by importin. This masking can be: (1) ___, whereby another protein binds and obscures the NLS, or (2) ___, whereby the protein itself folds in such a way that the signal is masked.
intermolecular, intramolecular
Unlike eukaryotic cells, prokaryotic cells do not have a nucleus. What are some possible benefits of the evolution of a nucleus in eukaryotes?
In contrast to prokaryotes, eukaryotic RNA is extensively modified by processes such as splicing and RNA editing, which are critical to the accurate transfer of genetic information from gene to protein. Sequestering the chromosomes in a separate compartment allows RNA-processing events to be more efficient, because the enzymes involved are sequestered in the nucleus and hence have less interference from unrelated enzymes. In addition, because RNA is retained in the nucleus until the processing events are complete, inappropriate translation of unprocessed RNAs does not occur. Furthermore, an additional level of control comes from the entry of regulated transcription factor into the nucleus. This would not be possible if the cytosol were ___ separated from the nucleus and chromosomes.
NOT
Protein transport into the endoplasmic reticulum (ER) or mitochondria requires unfolding the protein and threading the amino acid chain through a channel or pore into the organelle. In contrast, protein transport into the nucleus does not require an unfolding of the protein. Why is this not necessary for nuclear protein import?
The nuclear pore complex is a ___ structure composed of about 30 different pore proteins, and its central channel has a diameter of approximately 10–40 nm, which is large enough for even very large protein complexes. For this reason, it is unnecessary to unfold the protein, which can pass through the pore in its native state.
huge
