Terminology

40S - The small ribosomal subunit in eukaryotic cells. It contains the 18S rRNA.
60S - The large ribosomal subunit in eukaryotic cells. It contains the 28S, 5S, and 5.8S rRNAs.
80S - The complete eukaryotic ribosome, containing both a 40S and a 60S subunit, as well as associated rRNAs.
ACS - An 11-base pair sequence, 5'-TTTTATATTTT-3' found in multiple copies in a yeast ARS sequence.
Alternative Splicing - The splicing of a eukaryotic RNA transcript in different ways, to include or exclude certain exons from the final mRNA.
Alu Elements - A set of repeated sequences in the human genome that are each about 300 bp long. There of hundreds of thousands of copies of this sequence in the genome. They are inefficiently transcribed in the cell. Some of them may contain origins for DNA replication.
Anaphase - A part of the mitotic cell cycle when chromatids separate. (Figure 28.15)
Apoptosis - Programmed cellular death.
Autocatalysis - Refers to a reaction that an molecule catalyzes on part of its own structure.
Autonomously Replicating Sequences (ARSs) - Yeast DNA sequences essential for replication of plasmids.
Caspace Cascade - A cascade of proteolysis arising from the fact that the enzymes can cleave on the carboxyl side of aspartate and that this also is how the inactive precursor enzyme is activated.
Caspaces - A group of proteases that all cleave to the carboxyl side of aspartate (c-asp-ase) and are all synthesized as inactive precursors that can be activated by just such a cleavage. Thus, there is the possibility of a caspase cascade, once activation is triggered.
cdc2 - A serine/threonine kinase from yeast whose activation requires association with cyclins. One cyclin activates this protein at the start of S phase and another reactivates it at the beginning of mitosis.
Cell Cycle - A defined set of phases a cell goes through during the process of division.
Centromere - The region of a chromosome where the two sister chromatids are attached together. It is also the site of attachment for spindle fibers during mitosis and meiosis.
Chaperonins - Proteins involved in insuring that a newly synthesized protein remains unfolded.
Checkpoint for the Cell Cycle - In the yeast cycle, a requirement that the cdc2 protein, which must be phosphorylated at entry to G2, be dephosphorylated in order for mitosis to occur. If dephosphorylation has not happened at this point, mitosis is stopped.
Chromatin - The filamentous material of eukaryotic chromosomes, consisting of DNA with associated histones and other proteins. During interphase it is dispersed and fills most of the nucleus. During nuclear division it condenses into compact chromosomes.
Control Element - A DNA sequence that binds a transcription factor.
Cyclins - A group of proteins that associate with kinases involved in transition through the cell cycle.
Cytokinesis - The part of the mitotic cell cycle when the cell actually divides. Figure 28.16.
Diploid - Cells that contain two complete copies of the genome.
Docking Protein - A protein on the surface of the rough endoplasmic reticulum that binds the ribosome with the the protein with the signal sequence to the surface so the protein can be inserted in the membrane.
Enhancers - DNA sequences, as much as several kilobases away that can bind trans-acting factors and affect transcription of genes. Figure 28.23
Euchromatin - Regions of chromatin that are not as densely packed as heterochromatin and contain the regions where transcription can occur.
Exon - Regions of eukaryotic RNA that are put together by the action of splicing, and appear in the mature, final RNA.
G 0 - A term given to the G1 phase of the cell cycle for cells that are permanently arrested in G1.
Guide RNAs - Small RNAs required for the process of RNA editing.
Haploid - Cells that contain one complete copy of the genome.
Heme-Controlled Inhibitor (HCI) - A kinase that becomes activated when heme levels fall. It phosphorylates translational initiation factor eIF2, preventing recyling of eIF2 for initiation.
Heterochromatin - Highly condensed regions of chromatin that may be supercompacted into permanently coiled into 30 nm fibers. These are regions of the chromosome that are not transcriptionally active.
Histone Acetyltransferases - Enzymes that transfer an acetyl group to specific lysine residues in the N-terminal tails of nucleosomal proteins.
Histone Core Proteins - The proteins found in the core of a nucleosome -H2A, H2B, H3, and H4
Histone Deacetylases - Enzymes that remove an acetyl group from specific lysine residues in the N-terminal tails of nucleosomal proteins.
Histones - Five small, very basic proteins rich in lysine and arginine that are found in chromatin. Some have been remarkably well conserved in amino acid sequence throughout evolution. Table 28.1
Homeo Box - A common sequence element of about 180 base pairs that is found in homeotic genes. It codes for a sequence-specific DNA-binding element of the helix-loop-helix class.
Homeotic Genes - Genes that contain homeo box elements and typically are involved in controlling the pattern of organismal development. Homeotic mutations, which scramble portions of this pattern, affect homeotic genes. The nuclear DNA-binding proteins encoded by these genes presumably serve as transcriptional regulators for the coordinated expression of groups of genes.
Interferons - Anti-viral agents produced by cells in response to virus infections.
Interphase - The phase during which the G1, S, and G2 phases occur. During this time, DNA is replicated. Figure 28.16.
Introns - Regions of eukaryotic RNA that are edited out of the final RNA product by the action of splicing.
Linker DNA - A term describing the part of DNA located between successive nucleosomes in chromatin.
Matrix Attachment Regions (MARs) - The point at which DNA fragments are attached to the nuclear matrix. Figure 28.13.
Metaphase - A part of the mitotic cell cycle when each chromosome aligns independently at the metaphase plate. Figure 28.16
Metaphase Scaffolding - A structure in the nucleus that helps hold the folded metaphase chromosomes in place.
Molecular Parasites - A term used to describe sequences in a genome that appear to serve no useful function.
Nonhistone Chromosomal Proteins - A bewildering variety of proteins, such as polymerases and other nuclear enzymes, hormone receptor proteins, and regulatory proteins of many kinds that are found in the eukaryotic nucleus associated with DNA.
Nuclear Matrix (Nuclear Scaffold) - A protein web that is left in the nucleus when histones and other weakly bound proteins are removed and most of the DNA is digested away. It is presumed to act as an organizing scaffold for the chromatin.
Nucleosome - The first-order structural unit for the packing of DNA in chromatin, consisting of 146 bp of DNA wrapped 1.75 times around a core octamer of histone proteins. Successive nucleosomes are connected by stretches of linker DNA.
Origin of Replication - The place on a DNA molecule where replication is initiated.
Ploidy - Refers to a copy of the genome. Cells that are haploid have one copy of the genome. Cells that are diploid have two copies of the genome.
Polyploid - Cells that contain numerous complete copies of the genome.
Polytene Chromosome - An extra-thick chromosome that includes many parallel copies of the original DNA molecule; it is produced by repeated rounds of DNA replication without separation of the resulting copies.
Prophase - A part of the mitotic cell cycle during which chromosomes condense, the spindle forms, and the nuclear envelope disintegrates. Figure 28.16
Proteasomes - Proteolytic complexes that degrade ubiquitinated proteins.
Pseudogenes - Sequences in a eukaryotic genome (though some prokaryotes may have sequences like this too) that bear strong sequence similarity to functioning genes, from which they undoubtedly evolved. They are no longer transcribed, however, because some element required for transcription (often a flanking control region or promoter) is missing or defective.
Recognition Helix - The part of a helix-turn-helix protein that lies in the major groove of DNA.
RNA Editing - A process affecting mitochondrial mRNAs of some unicellular eukaryotes, which involves insertion or deletion of uridine residues into messages during the processing steps. Apparently, the insertions are made by a kind of reverse splicing mechanism, and only at certain points.
RNA Polymerase I - A large, complex enzyme with 13 subunits responsible for synthesizing the large 45S pre-rRNA transcript of eukaryotic cells. This transcript is later processed into mature 28S, 18S, and 5.8S ribosomal RNAs (rRNAs).
RNA Polymerase II - The RNA polymerase in eukaryotes that transcribes all protein-coding genes. It also transcribes some small nuclear RNAs involved in splicing.
RNA Polymerase III - The most complex of the eukaryotic RNA polymerases, with 14 subunits. It transcribes small RNAs, such as tRNAs and the 5S ribosomal RNA.
Satellite DNA - A type of repeating sequence in eukaryotic DNA involving multiple tandem repetitions, over long stretches of DNA, of very short, simple sequences like (ATAAACT)n. Figure 28.3
Signal Recognition Particles (SRPs) - Complexes of several proteins and a small (7SL) RNA involved in transporting proteins to the Golgi apparatus. They recognize the signal sequences of the appropriate nascent proteins and bind to them as they are being extruded from the ribosomes.
Small Nuclear Ribonucleoprotein Particles (snRNPs) - snRNA-protein complexes that splice RNAs in eukaryotic cells.
Small Nuclear RNAs (snRNAs) - A group of small RNAs found in the nucleus that function in the process of splicing of RNAs.
SNARES - Proteins in the membranes of a vesicle that matches a complementary protein in the target membrane.
Spliceosome - The snRNP-pre-mRNA complex.
Telomerase - An enzyme in eukaryotic cells that elongates telomeres shorted by repeated rounds of replication.
Telomere - A structure at the end of linear eukaryotic chromosomes. The DNA sequence consists of simple tandemly repeated sequences usually with one strand is G-rich, the other C-rich.
Telophase - A part of the mitotic cell cycle when the nuclear envelope reforms. Figure 28.16
Transcription Factors - Proteins that influence the transcription of particular genes, usually by binding to specific promoter sites.
Ubiquitin - A 76-residue polypeptide used to mark a protein for degradation