Category - Definitions

Query - What definition best describes the term below?

Reversal

Category - Term Recognition

Query - What term does the description below refer to?

(Terms are shown on left, descriptions in middle, figures on right)

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 repeated sequence in the human genome that is 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 one 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 that are involved in managing the folding of other proteins. Some of them help proteins to fold correctly; some prevent premature folding; and some prevent polypeptides from associating with other polypeptides until they have folded properly. |  | 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 28.15 | 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. |  | G0 | 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 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 28.15 | 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 28.15 | 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 |  | 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 28.15 | 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 |  | Telophase | A part of the mitotic cell cycle when the nuclear envelope reforms. | Figure 28.15 | 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 |

Category - General

Query - Is contained in the left column below, solution in middle, figure on right

Reversal - there is no reversal

Above the level of the nucleosome, what are the next levels of folding in chromatin? | The beaded fiber is folded into a thicker fiber and then these fibers are folded further to make the thicker chromatin fibers visible in both metaphase chromosomes and the nuclei of nondividing cells. |  | During interphae, what is the status of the chromatin? | It is dispersed throughout the nucleus and is actively engaged in transcription. |  | How are groups of coordinately expressed genes arranged in the nuclear matrix? | Between adjacent MARs |  | How are tRNA genes organized in eukaryotes? | They are present in multiple copies, but are usually not grouped together in tandem arrays, nor are they localized in one region of the nucleus. Rather, they are scattered over the genome and throughout the nucleus. |  | How can the compactness of chromatin be measured with a nuclease? | Tightly packed chromatin (heterochromatin) will provide little access of the nuclease to the DNA, resulting in little cleavage. Loosely packed chromatin will have more exposed DNA and when treated with a nuclease will yield more cut sites on the DNA. |  | How do eukaryotic cells compensate for the much larger genome sizes and slower DNA replication rates than prokaryotic cells? | By utilizing many origins of replication |  | How do Okazaki fragments differ between prokaryotes and eukaryotes? | In size. They are much smaller in eukaryotes - about 135 bases long. |  | How does cycloheximide inhibit eukaryotic translation? | It inhibits the peptidyltransferase activity of the ribosome. |  | How does development affect gene copy number? | For genes, such as the globins, different forms of a gene may be required at different points in life, necessitating different forms of the gene to be present in the genome. |  | How does diphtheria toxin inhibit eukaryotic translation? | It catalyzes a reaction in which NAD+ adds an ADP ribose group to a specially modified histidine in the translocation factor eEF2, the eukaryotic equivalent of EF-G |  | How does replication through nucleosomal regions occur? | It seems likely that nucleosomes from the parental chromatin strand are disassembled ahead of the replication fork and are then reassembled on one or the other of the daughter strands | Figure 28.17 | How does telomerase manage to lengthen the telomeres at the end of the linear eukaryotic chromosomes? | It contains a small RNA that it uses as a primer for replication. |  | How does the chromatin structure of the globin genes change during development? | Before globin is synthesized, it is densely covered with nucleosomes. At differentiation, a looser structure is observed, as measured by susceptibility of the DNA to nucleases, indicating it is not completely covered with protein. |  | How does the length of DNA between histones vary? | From about 20 to over 100 base pairs. |  | How does transcription by RNA Polymerase II differ from transcription by the prokaryotic RNA polymerase? | RNA Polymerase II cannot initiate transcription without the assistance of other protein factors. |  | How is the cap of eukaryotic mRNAs made? | A GTP residue is added in reverse orientation and forms, together with the first two nucleotides of the chain, the cap. It is "decorated" by addition of methyl groups to the N-7 position of the guanine and to one or two sugar hydroxyl groups of the cap nucleotides. |  | How many base pairs are in a nucleosome? | 146 |  | How many base pairs of DNA are devoted to the various globin genes in the human genome? | About 100,000 |  | How many nonhistone chromosomal proteins can be found in a typical nucleus? | Approximately 1000 |  | How many ribosomal RNAs are found in eukaryotic cells? | Four - the 18S rRNA in the small ribosomal subunit, and the 28S, 5.8S and 5S rRNAs in the large ribosomal subunit. |  | How many times are some sequences repeated in eukaryotic genomes? | 100,000 to 1,000,000 times |  | How many times does DNA wrap around a nucleosome? | 1.75 times. |  | How much much more DNA is in eukaryotic genomes than the genome of E.coli? | Most eukaryotic cells have genomes 100 to 10,000 fold larger. For other eukaryotes like yeast, the difference may be as small as 2 fold larger. |  | In a typical differentiated eukaryotic cell, what percentage of the total DNA is typically ever transcribed? | 5%-10% |  | In addition to binding the region of the DNA near the 5S rRNA gene, what other nucleic acid does TFIIIA bind? | The 5S rRNA |  | In higher eukaryotes, what percentage of the genome is taken up by satellite DNA? | 10% to 20% |  | Once a cell has fully differentiated, it may either divide very slowly or never again. Which phase of the cell cycle is elongated (or made permanent) for a cell like this? | G1 |  | What advantage does alternative splicing provide in terms of economy of coding sequences? | Multiple proteins can be made from a relatively small set of sequences, instead of having a separated gene for each possible protein produced by alternative splicing. |  | What are the beads seen in electron micrographs of chromatin? | Nucleosomes |  | What are the common structural motifs found in DNA-binding transcription factors? | Zinc finger motifs, helix-turn-helix motifs, leucine zippers |  | What are the phases of mitosis? | Prophase, metaphase, anaphase, telophase, and cytokinesis | Figure 28.15 | What are the three protein transcription factors required for expression of the 5S rRNA genes by RNA Polymerase III? | TFIIIA, TFIIIB, and TFIIIC. | Figure 28.21 | What are two functions of the signal recognition particles (SRPs) in protein targeting? | 1. Inhibit translation by binding the signal sequences of newly synthesized proteins as they emerge from the ribosome 2. Recognize and bind to a docking protein in the rough endoplasmic reticulum membrane. |  | What can trigger action of caspases? | Interferon, tumor necrosis factor. |  | What causes the chromatin of the ovalbumin, ovomucoid and lysozyme genes of chicken to become more sensitive to nucleases? | Estrogen |  | What chemical reactions trigger the successive stages of the cell cycle? | Phosphorylation of a number of nuclear proteins, including histone H1 |  | What chromosomal location has a high concentration of satellite DNA? | Centromere |  | What classes of proteins are found among the nonhistone chromosomal proteins? | Polymerases and other nuclear enzymes, hormone receptor proteins, and regulatory proteins of many kinds |  | What common feature of chromatin is not found in nucleolar chromatin? | Nucleosomes |  | What common structural motif of DNA-binding proteins is found in TFIIIA? | Zinc fingers |  | What compaction must be done to fit eukaryotic DNA into cells? | The length of the total DNA content of a human cell is nearly 3 meters, yet must be packed into a nucleus about 10-5 m in diameter. |  | What evolutionary function may introns play? | Serving as loci for genetic recombination, allowing functional parts of proteins to be interchanged in evolution. Such loci also allow some eukaryotes to make variants of a protein from a single gene, by splicing different exons together. |  | What forces hold together dimeric DNA binding proteins with a regular pattern of leucine or other hydrophobic residues (with 7-fold periodicity)? | Leucine zippers |  | What form do most eukaryotic chromosomes take? | The cell typically has several or many chromosomes, each of which contains a single, very large, linear DNA molecule. In nondividing cells, the chromosomes are segregated within the nucleus as an entangled mass of fibers of a DNA-protein complex called chromatin. |  | What form do most prokaryotic chromosomes take? | Almost all of the DNA is contained in a single, large, supercoiled circular DNA molecule, with a minor fraction in small plasmids. It exists free in the cytosol, although attached at one or more points to the cell membrane. |  | What function does the cap have in translation? | It serves to position the mRNA on the ribosome for translation. |  | What functional role is performed by multiple copies of a gene? | It may be useful for high levels of production of much-needed transcripts, such as those of the rRNA genes. |  | What gene normally not expressed in the mature cells is found in cancer cells and in immortalized tissue culture cells? | Telomerase |  | What happens in the cell cycle if p53 senses damage to the cell? | It activates transcription of the PIC1 gene, the product of which binds to the CDC kinases, blocking the cell in G1 and frequently leading to apoptosis. |  | What happens to mRNAs lacking a polyA tail? | They typically have shorter lifetimes in the nucleus. |  | What is an interesting structural feature of the DNA in the transcriptional initiation complex involving RNA Polymerase II? | It has a very prominent kink. |  | What is different about the amino acid used in translational initiation in prokaryotes and eukaryotes? | Both use methionine, but the eukaryotic methionine is not formylated as the prokaryotic one is. |  | What is involved in an RNA polymerase II transcriptional initiation complex? | RNA Polymerase II and at least five additional protein factors. |  | What is the part of the cell cycle encompassing phases G1, S, and G2 called? | Interphase |  | What is the rate of DNA replication in eukaryotes? | About 75 nucleotides per second. |  | What is the relationship between the genome size of an organism and its complexity? | There is no known relationship |  | What is the repeating unit of chromatin called? | The nucleosome. |  | What is the second checkpoint in the cell cycle? | When the protein p53 detects DNA damage. |  | What is the signal in the pre-mRNA used to specify polyadenylation? | AAUAAA |  | What is the structure of a yeast ARS sequence? | They are typically several hundred base pairs in length with subsequences carrying copies of an 11 bp consensus sequence, called ACS - 5' TTTTATATTTT 3', which is absolutely required for function. ARSs have binding sites for the six-polypeptide origin binding factor as well as a strong affinity for the nuclear matrix. |  | What is unique about the 28S rRNA of the protozoan Tetrahymena? | Excision and splicing of the intron near its 3' end is autocatalytic - the RNA catalyzes the reaction upon itself. | Figure 11.30 | What patter does chromatin have as viewed in the electron microscope? | It is beaded. |  | What percentage of mammalian DNA is single copy sequences? | About half |  | What protein must be dephosphorylated at entry to mitosis? | cdc2 |  | What protein must be phosphorylated at entry to the G2 phase of the cell cycle? | cdc2 |  | What protein-DNA complex in the eukaryotic cell is essential for both compacting the DNA into the confines of the nucleus and controlling the complex states of gene expression? | Chromatin |  | What proteins are cleaved by caspases? | Structural proteins, like actin and nuclear lamin, transcription factors, and splicing factors. |  | What proteins are involved in regulating entry of the cell into S-phase? | CDK2 and Cyclins A and E |  | What proteins are involved in the entry to mitosis? | cdc2 and cyclins A and B |  | What role do snRNAs play in splicing? | They recognize and bind intron–exon splice sites by means of complementary sequences |  | What small RNA involved in protein transport has it been proposed that the Alu sequences were derived from? | 7SL RNA |  | What structure does the spliced intron have when splicing is complete? | A lariat. |  | What translational inhibitors that work in prokaryotic cells also function in eukaryotic cells? | Pactamycin, tetracycline, and puromycin |  | What two major structural features at the 5' end of mRNAs distinguish eukaryotic and prokaryotic messages? | 1. Prokaryotic mRNAs have Shine-Dalgarno sequences and eukaryotes do not. 2. The 5' ends of eukaryotic mRNAs have a cap structure and prokaryotic mRNAs do not. |  | Where are the globin genes exclusively expressed in the body? | In the erythropoietic cells that give rise to red blood cells. |  | Where are the multiple genes for the 45S pre-rRNA of eukaryotes located? | Nucleolus |  | Where do proteins get glycosylated first in the cell? | In the lumen of the rough endoplasmic reticulum |  | Where does capping, splicing, and polyadenylation of mRNAs occur? | In the nucleus. |  | Where on a protein exported to another cellular organelle, is the targeting sequence? | At the N-terminus. |  | Which chaperone proteins are involved in transporting proteins into the mitochondrion? | Members of the 'heat shock' HSP70 family |  | Which DNA polymerases are used during S phase replication of eukaryotic cells? | , delta, and |  | Which eukaryotic rRNA has no counterpart in prokaryotes? | 5.8S rRNA |  | Which histones are found in the core octamer of a nucleosome? | Two copies each of H2A, H2B, H3, and H4 |  | Where is histone H1 found in chromatin? | It is associated with linker DNA and helps form higher-order structures. |  | Which of the three transcription factors used by RNA polymerase III is specific only for the 5S rRNA genes? | TFIIIA | Figure 28.21 | Which prominent eukaryotic mRNAs lack a poly(A) tail? | Most mRNAs for the histones. |  | Which regions of eukaryotic chromosomes tend to replicate early? | Transcriptionally active regions. |  | Why do eukaryotic telomeres shorten? | DNA polymerases are unable to replicate at the 5' ends of linear DNAs, since they absolutely require a primer. Each round of replication, a little portion of the linear end is lost for this reason. |  | Why does the DNA sequence of pseudogenes appear to change much faster than the corresponding active genes? | Pseudogenes are under no selective pressure against mutation. |  | Why is DNA replication slower in eukaryotes than in prokaryotes? | The nucleosome machinery must apparently be dismantled and then reconstructed on the daughter DNA molecules as the replication machinery proceeds. |

How are the DNA-binding proteins of chromatin classified? | Histones - small very basic proteins rich in lysine and arginine remarkably conserved through evolution. Nonhistone chromosomal proteins - includes a bewildering variety of proteins, including polymerases, other nuclear enzymes, hormone receptor proteins, and numerous regulatory proteins. |  | How are the phases of the cell cycle defined? | G1 Phase (or first gap phase) - follows cell division. Cells are diploid. Late in the phase the commitment to divide may be triggered. S Phase - Preparation for division begins - DNA is replicated and the histones and nonhistone proteins are deposited on the daughter DNA molecules to reproduce the chromatin structures.

G2 phase - Replication is complete and cell is tetraploid.

M Phase - This is when mitosis occurs and is divided into prophase, metaphase, anaphase, telophase, and cytokinesis.

What are the steps in eukaryotic mRNA trascription initiation?

1. The pre-initiation complex forms.

2. Melting of a short region of DNA and initiation of transcription.

3. The C-terminal tail of RNA Polymerase II becomes strongly phosphorylated and transcription begins, with a helicase unwinding DNA strands ahead of the polymerase complex.

4. A number of the core transcription factors are released and RNA Polymerase II, together with TFIIF move along the DNA. A residual complex, containing TBP, TFIIA, TAFs and probably activator proteins, remains at the start site, ready to initiate another round of transcription.

5. The RNA Polymerase II acquires several special elongation factors, some of which assist the enzyme in dealing with pause sites in the DNA. The accessory proteins (which include nucleosome remodling factors and a specific elongation factor called FACT) also help RNA Polymerase II to pass through nucleosomal arrays in in vitro studies.

How does termination of eukaryotic mRNA transcription proceed?

1. The eukaryotic RNA polymerase II usually continues to transcribe well past the end of the gene.

2. After the end of the gene has been reached, RNA polymerase II passes through one or more AATAAA sequences in the DNA, which lie beyond the 3' end of the coding region.

3. The pre-mRNA, carrying this signal as AAUAAA, is then cleaved by a special endonuclease that recognizes the signal and cuts at a site 11 to 30 residues 3' to it.

4. A tail of polyriboadenylic acid, poly(A), as much as 200 bases long, is added by a special non-template-directed polymerase.

What is the sequence of reactions in splicing?

1. Attachment of the U1 snRNP to the G site at the 5' end of the intron.

2. The U2 snRNP attaches at the branch site.

3. Assembly of the spliceosome continues, including addition of several more snRNPs

4. The lariat loop in the intron is formed and the two exons are joined. Splicing has now been accomplished, and the products-a ligated mRNA and a looped intron-are released. As the spliceosome disintegrates, the looped intron is degraded, and the mRNA is exported from the nucleus.

What mechanisms do eukaryotic cells used to regulate translation?

1. Sequestering of specific mRNAs by combination with specific mRNA-binding proteins

2. Rapid degradation of mRNA so that they do not persist in inappropriate phases of the cell cycle

3. Phosphorylation of factors involved in translation

How do interferons control eukaryotic translation?

1. By stimulating mRNA degradation

2. By inducing the synthesis of a protein kinase that phosphorylates eIF2

How are proteins targeted for the Golgi apparatue delivered there?

1. Synthesis begins when an N-terminal hydrophobic signal sequence is synthesized by ribosomes on cytoplasmic mRNA.

2. Signal recognition particles (SRPs), containing several proteins and a small (7SL) RNA, recognize the signal sequences of the appropriate nascent proteins and bind to them as they are being extruded from the ribosomes. The SRP temporarily halts translation, so that no more than the N-terminal signal sequence extends from the ribosome and recognizes a docking protein in the RER membrane.

3. The docking protein binds the ribosome to the RER, and the signal sequence is inserted into the RER membrane.

4. The SRP is released, allowing translation to resume.

5. The protein being synthesized is actually pulled through the membrane by an ATP-dependent process.

6. Before translation is complete, signal sequences are cleaved from some proteins by an RER-associated protease. These proteins are released into the lumen of the RER and further transported. Proteins that will remain in the endoplasmic reticulum have resistant signal peptides and thereby remain anchored to the RER membrane.

What two distinct methods do eukaryotic cells employ for protein degradation?

1. The lysosomal system

2. The cytosolic degradation system

How is ubiquitin attached to a protein?

1. Ubiquitin's carboxyl group is activated by thiol coupling to an activating enzyme in an ATP-dependent process.

2. The ubiquitin moieties are then transferred to a second enzyme

3. The second enzyme attaches ubiquitin to -amino groups of lysine residues on the fated protein.

Category - General

Query - What is the approximate size of the following genome in base pairs?

Reversal - there is no reversal

(genomes on left, size in middle, figure on right)

E.coli | 5 x 106 | Figure 28.1 | Yeast | 1.2 x 107 | Figure 28.1 | Insect | 1 x 10 8 | Figure 28.1 | Mammal | 1 x 109 | Figure 28.1

Category - General

Query - What are the identified functions of the human transcription initiation factor below?

Reversal - there is no reversal

(initiation factor on left, functions in middle, figure on right)

TFIID | Encompasses TBP and TAFs |  | TFIIA | Stabilization of TBP binding; stabilization of TAF-DNA interactions; anti-repression functions. |  | TFIIB | RNA Polymerase II-TFIIF recruitment; start-site selection by RNA Polymerase II |  | TFIIF | Promoter targeting of Pol II; destabilization of non-specific RNA Polymerase II-DNA interactions |  | TFIIE | TFIIH recruitment; modulation of TFIIH helicase, ATPase, and kinase activities; direct enhancement of promoter melting |  | TFIIH | Promoter melting using helicase activity |  | RNA Polymerase II | Catalytic functions in RNA synthesis; recruitment of TFIIE |  | TBP | Core promoter recognition (TATA) |  | TAFs | Core promoter recognition (non-TATA elements); positive and negative regulatory functions. |

Category - General

Query - What is the function of the eukaryotic translational initiation factor below?

Reversal - there is no reversal

(initiation factor on left, functions in middle, figure on right)

eIF1, eIF1A | Search for the first AUG and in forming the initiation complex |  | eIF2, eIF2B | Involved in forming the initiation complex |  | eIF3, eIF4C | Involved in forming the initiation complex |  | eIF4A, eIF4B, eIF4F | Involved in the search for the first AUG |  | eIF5 | Helps dissociate eIF2, eIF3, eIF4C |  | eIF6 | Helps dissociate 60S subunit from inactive ribosomes. |  | eEF1 | Delivery of aminoacyl tRNA to ribosomes |  | eEF1 | Aids in recycling eEF1 |  | eEF2 | Translocation factor |  | eRF | Release of the complete polypeptide chain. |