Term
| About ___ genes are expressed at widely differing levels in a eukaryotic cell |
|
Definition
|
|
Term
| mRNAs expressed at low levels.. |
|
Definition
| overlap extensively when different cell types are compared |
|
|
Term
|
Definition
| a gene that is (theoretically) expressed in all cells because it provides basic functions needed for sustenance of all cell types |
|
|
Term
| Six steps in microarray production |
|
Definition
1) Create probes from cDNA libraries to be placed on chips
2) Sequenced probes are then placed on slides using a robotic spotter
3) Isolate mRNA from cells of interest
4) Label expressed genes Red or Green
5) Place in buffer solution containing your chip
6) Analyze using digital imaging |
|
|
Term
| Microarray technology is a representation of... |
|
Definition
|
|
Term
| What are four methods of transcriptome sequencing? |
|
Definition
RNA-seq
Illumina GA
Illumina High-Seq
Roche 454 |
|
|
Term
| Premise behind hibernation experiments? |
|
Definition
Hibernation is controlled by the differential expression of specific genes
These same genes are found in all mammals, including humans |
|
|
Term
| During mammalian hibernation, what is always working? Sometimes working? Fuel for both? |
|
Definition
Always: Heart muscle
Sometimes: Skeletal muscle
Fuel: White adipose |
|
|
Term
| What temperature were ground squirrels at during torpor (January) |
|
Definition
|
|
Term
| What is the ground squirrel hibernation period? |
|
Definition
|
|
Term
|
Definition
Specialized for heat production
Contain a high density of mitochondria |
|
|
Term
| How was the brown adipose tissue transcriptome identified? |
|
Definition
|
|
Term
Compare 454 of WAT, heart and skeletal muscle vs. Illumina High Seq of BAT:
Read length |
|
Definition
454: 335 bp
Illumina: 100 bp |
|
|
Term
Compare 454 of WAT, heart and skeletal muscle vs. Illumina High Seq of BAT:
Total reads |
|
Definition
454: 3.7 million
Illumina: 180 million |
|
|
Term
Compare 454 of WAT, heart and skeletal muscle vs. Illumina High Seq of BAT:
Total bases sequenced |
|
Definition
454: 1.3 billion
Illumina: 18 billion |
|
|
Term
Compare 454 of WAT, heart and skeletal muscle vs. Illumina High Seq of BAT:
Availability of I. tridecemlineatus genome |
|
Definition
454: 2x coverage, Sanger sequencing
Illumina: 80x Coverage, Illumina sequencing ~98% complete |
|
|
Term
| The functional information of a gene is in the.. |
|
Definition
|
|
Term
| Four uses for proteomics? |
|
Definition
1) Proteome profiling
2) Comparative expression analysis of 2 or more protein samples
3) Localization and identification of post-translational modifications
4) Protein-protein interactions |
|
|
Term
| _____ is the primary tool for protein identification |
|
Definition
|
|
Term
| Mass spectrometry is a powerful analytical technique that... |
|
Definition
| produces spectra of the masses of the atoms or molecules comprising a sample |
|
|
Term
| What are the spectra of a mass spec reading used for? |
|
Definition
| to determine the elemental or isotopic signature of a sample, the masses of particles or molecules, and to elucidate the chemical structures of molecules, such as peptides |
|
|
Term
| How does a mass spec work? |
|
Definition
| ionizing chemical compounds to generate charged molecules and measuring their mass-to-charge ratios |
|
|
Term
| Analysis of proteins by MS occurs in what three major steps? |
|
Definition
1) Ionization
2) Separation by m/z
3) Detection |
|
|
Term
| How are proteins ionized? |
|
Definition
1) MALDI
2) Electrospray (liquid chromotography or nanospray) |
|
|
Term
| How are proteins separated by m/z? |
|
Definition
1) Time of flight
2) Ion trap
3) Quadropole |
|
|
Term
| What does the detection step involve? |
|
Definition
| Mass analysis of proteins and peptides |
|
|
Term
|
Definition
| Matrix Assisted Laser Desorption/Ionization |
|
|
Term
|
Definition
|
|
Term
|
Definition
| Evaporation and charge transfer to MS via laser light |
|
|
Term
|
Definition
Spray through ESI needle
Repeated evaporation steps until charged molecule enters mass spec |
|
|
Term
|
Definition
Laser excites molecules
Go through flight tube
Hit laser detector (light molecules fly fastest) |
|
|
Term
|
Definition
Tandem mass spec
Isolates already isolated particles further using argon gas |
|
|
Term
| Eukaryotic gene expression is usually controlled at the... |
|
Definition
| level of initiation of transcription by opening the chromatin |
|
|
Term
|
Definition
| Changes that influence the phenotype without altering the genotype |
|
|
Term
|
Definition
| the energy-dependent displacement or reorganization of nucleosomes that occurs in conjunction with activation of genes for transcription |
|
|
Term
| What happens if nucleosomes form at a promoter? |
|
Definition
| Transcription factors and DNA polymerase can't bind |
|
|
Term
| Chromatin remodeling is dependent on... |
|
Definition
| ATP to displace nucleosomes from specific DNA sequences |
|
|
Term
| All chromatin remodeling complexes contain... |
|
Definition
| a related ATPase catalytic subunit and are grouped into subfamilies containing more closely related ATPase subunits |
|
|
Term
| Remodeling complexes can ___, ____, or ___ nucleosomes. |
|
Definition
| Alter, slide, or displace |
|
|
Term
| Some remodeling complexes can... |
|
Definition
| exchange one histone for another in a nucleosome |
|
|
Term
| Remodeling complexes can be classified by their... |
|
Definition
|
|
Term
| What does SWI/SNF stand for? |
|
Definition
| Switch/Sucrose Non-Fermenting |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| What happens if you remove an acetyl group? |
|
Definition
| Transcriptional repression |
|
|
Term
| In microarrays, Cy3 is what and Cy5 is what? |
|
Definition
|
|
Term
| A remodeling complex does not itself have specificity for any particular target site but must be... |
|
Definition
| recruited by a component of the transcription apparatus |
|
|
Term
| Remodeling complexes are recruited to promoters by... |
|
Definition
| sequence-specific activators |
|
|
Term
| Once the remodeling complex has bound, |
|
Definition
| the sequence-specific factor may be released |
|
|
Term
| Transcription activation often involves... |
|
Definition
| nucleosome displacement at the promoter |
|
|
Term
|
Definition
| nucleosome-free regions flanked by nucleosomes containing the H2A variant H2AZ (Htz1 in yeast) |
|
|
Term
| The MMTV promoter requires... |
|
Definition
| a change in rotational positioning of a nucleosome to allow an activator to bind to DNA on the nucleosome |
|
|
Term
| Histone acetylation is associated with... |
|
Definition
| activation of gene expression |
|
|
Term
| Newly synthesized histones are acetylated at specific sites and then... |
|
Definition
| deacetylated after incorporation into nucleosomes |
|
|
Term
| What does lysine acetyltransferase (KAT) do? |
|
Definition
| Typically present in large complexes, it acetylates lysine residues in histones (or other proteins). Also known as HAT |
|
|
Term
| ___ ___ are associated with histone acetylase activities in large complexes. |
|
Definition
|
|
Term
| Histone deacetylase (HDAC) |
|
Definition
| Enzyme that removes acetyl groups from histones, may be associated with repressors of transcription |
|
|
Term
|
Definition
| used to recognize acetylated sites on histones |
|
|
Term
|
Definition
| used to recognize methylated lysines in histones |
|
|
Term
| Deacetylation is associated with... |
|
Definition
| repression of gene activity |
|
|
Term
| Deacetylases are present in... |
|
Definition
| complexes with repressor activity |
|
|
Term
| ____ is a feature of inactive chromatin |
|
Definition
| Methylation of both DNA and specific sites on histones |
|
|
Term
| The ___ domain is part of the catalytic site of protein methyltransferases. |
|
Definition
|
|
Term
| _____ and other conserved domains can bind to specific methylation sites on histones. |
|
Definition
|
|
Term
| Methylation of histones and methylation of DNA are... |
|
Definition
|
|
Term
| ____ can recruit chromatin modifying complexes |
|
Definition
|
|
Term
| Different modifications and complexes facilitate... |
|
Definition
|
|
Term
| Histone phosphorylation is linked to... |
|
Definition
| transcription, repair, chromosome condensation, and cell cycle progression |
|
|
Term
| Epigenetic effects can result from... |
|
Definition
| modification of a nucleic acid after it has been synthesized or by the perpetuation of protein structures |
|
|
Term
| Heterochromatin is nucleated at a specific sequence, and... |
|
Definition
| the inactive structure propagates along the chromatin fiber |
|
|
Term
| Genes within regions of heterochromatin are... |
|
Definition
|
|
Term
| Position effect variegation (PEV) is... |
|
Definition
| inactivation of genes in the vicinity of an inactive heterochromatin region |
|
|
Term
| Heterochromatin spreadying continues until... |
|
Definition
| proteins required for heterochromatin are depleted or an obstacle is encountered |
|
|
Term
| Similar processes to heterochromatin spreading occur at... |
|
Definition
| telomers (telomeric silencing) and the silent cassettes in yeast mating type |
|
|
Term
| ___ is the key protein in forming mammalian heterochromatin, and acts by binding to _____ |
|
Definition
|
|
Term
|
Definition
| initiates formation of heterchromatin in yeast by binding to specific target sequences in DNA |
|
|
Term
| The targets of Rap1 include... |
|
Definition
| telomeric repeats and silencers at HML and HMR |
|
|
Term
|
Definition
| Sir3/Sir4, which interact with the N-terminal tails of H3 and H4 |
|
|
Term
|
Definition
| deacetylates the N-terminal tails of H3 and H4 and promotes spreading of Sir3/Sir4 |
|
|
Term
| ___ promote heterochromatin formation at centromeres. |
|
Definition
|
|
Term
| Polycomb group proteins (Pc-G)... |
|
Definition
| perpetuate a state of repression through cell divisions |
|
|
Term
|
Definition
| a DNA sequence required for the action of Pc-G |
|
|
Term
|
Definition
| nucleation center from which Pc-G proteins propagate an inactive structure |
|
|
Term
| Trithorax group proteins... |
|
Definition
| antagonize the actions of the Pc-G |
|
|
Term
| ____ is necessary for transcription. |
|
Definition
| Demethylation at the 5' end of the gene |
|
|
Term
| _____ surround the promoters of some genes |
|
Definition
|
|
Term
| There are _____ CpG islands in the human genome; ____ exist outside Alu elements |
|
Definition
|
|
Term
| Methylation of a CpG island prevents... |
|
Definition
| activation of a promoter within it |
|
|
Term
| ____ is caused by proteins that bind to methylated CpG doublets |
|
Definition
|
|
Term
| Replication converts a fully methylated site to a... |
|
Definition
|
|
Term
| de novo methyltransferase |
|
Definition
| Adds a methyl group to an unmethylated target sequence on DNA |
|
|
Term
| maintenance methyltransferase |
|
Definition
| converts hemimethylated sites to fully methylated sites |
|
|
Term
| DNA and histone methylation are... |
|
Definition
|
|
Term
| ____ stabilizes inactive chromatin via CpG methylation and HP1 loading onto methylated H3K9 |
|
Definition
|
|
Term
|
Definition
| the process of excising introns from RNA and connecting the exons into a continuous mRNA |
|
|
Term
|
Definition
| the nuclear primary transcript that is processed by modification and splicing to give an mRNA |
|
|
Term
|
Definition
| the ribonucleoprotein form of hnRNA (heterogeneous nuclear RNA), in which the hnRNA is complexed with proteins |
|
|
Term
| Where are pre-mRNAs found? |
|
Definition
|
|
Term
|
Definition
| RNA that comprises transcripts of nuclear genes made by RNA pol II; it has a wide size distribution and low stability |
|
|
Term
| The 5' end of eukaryotic mRNA is... |
|
Definition
|
|
Term
| The 5' cap of euk mRNA is formed by.. |
|
Definition
| adding a G to the terminal base of the transcript via a 5'-5' link |
|
|
Term
| The cap blocks the 5' end of mRNA and can be... |
|
Definition
| methylated at several positions |
|
|
Term
|
Definition
| sequences immediately surrounding the exon-intron boundaries. They are named for their positions relative to the intron |
|
|
Term
| The 5' splice site includes the consensus sequence.. |
|
Definition
|
|
Term
| The 3' splice site includes the consensus sequence... |
|
Definition
|
|
Term
| Splice junctions are read... |
|
Definition
|
|
Term
| Splicing depends only on... |
|
Definition
| recognition of pairs of splice junctions |
|
|
Term
| All 5' splice sites are... |
|
Definition
| functionally equivalent (same for 3' sites too) |
|
|
Term
| Additional conserved sequences at both 5' and 3' splice sites define... |
|
Definition
| functional splice sites among numberous other potential sites in the pre-mRNA |
|
|
Term
| The 3' ends of mRNAs are generated by... |
|
Definition
| cleavage and polyadenylation |
|
|
Term
| The sequence ______ is a signal for cleavage to generate a 3' end of mRNA that is polyadenylated |
|
Definition
|
|
Term
| The polyadenylation reaction requires... |
|
Definition
| a protein complex that contains a specificity factor, an endonuclease, and poly(A) polymerase (PAP) |
|
|
Term
| The specificity factor and endonuclease cleave RNA... |
|
Definition
|
|
Term
| The specificity factor and PAP add... |
|
Definition
| ~200 A residues processively to the 3' end |
|
|
Term
| The poly(A) tail controls... |
|
Definition
| mRNA stability and influences translation |
|
|
Term
|
Definition
| the region in an mRNA between the start of the message and the first codon |
|
|
Term
|
Definition
| the region in an mRNA between the termination codon and the end of the message |
|
|
Term
|
Definition
| a secondary structure that appears in RNAs consisting of a base-paired region (stem) and a terminal loop of single stranded RNA |
|
|
Term
| mRNA instability is due to the action of... |
|
Definition
|
|
Term
|
Definition
| cleaves RNA at internal sites |
|
|
Term
|
Definition
| removes terminal ribonucleotides from RNA |
|
|
Term
|
Definition
| an enzyme that remains associated with the substrate while catalyzing the sequential removal of nucleotides |
|
|
Term
|
Definition
| an enzyme that catalyzes the removal of only one of a few nucleotides before dissociating from the substrate |
|
|
Term
| mRNAs exhibit a wide range of... |
|
Definition
|
|
Term
|
Definition
| mRNA degradation, assuming that the degradation process is stochastic |
|
|
Term
| _____ is an important contributor to mRNA abundance and therefore the spectrum of proteins made in a cell |
|
Definition
| Differential mRNA stability |
|
|
Term
| steady state (molecular concentration) |
|
Definition
| the concentration of population of molecules when the rates of synthesis and degradation are constant |
|
|
Term
|
Definition
| a changing population of proteins during its nuclear maturation and cytoplasmic life |
|
|
Term
| Some nuclear-acquired _____ have roles in the cytoplasm |
|
Definition
|
|
Term
| A very large number of ______ exist, most of which remain uncharacterized |
|
Definition
| RNA-binding proteins (RBPs) |
|
|
Term
| Different mRNAs are associated with distinct, but overlapping, sets of regulatory proteins, creating... |
|
Definition
|
|
Term
|
Definition
| an mRNA that is simultaneously being translated by multiple ribosomes |
|
|
Term
|
Definition
| mRNA that codes for one polypeptide |
|
|
Term
| Degradation of bacteria mRNAs is initiated by... |
|
Definition
| removal of a pyrophosphate from the 5' terminus |
|
|
Term
| Describe the degradation of monophosphorylated mRNAs in proks. |
|
Definition
| Degraded during translation in a two step cycle involving endonucleolytic cleavages, followed by 3' to 5' digestion of the resulting fragments |
|
|
Term
| The modifications at both ends of mRNA protect is from... |
|
Definition
| degradation by exonucleases |
|
|
Term
| poly(A) binding protein (PABP) |
|
Definition
| the protein that binds to the 3' stretch of poly(A) on a eukaryotic mRNA |
|
|
Term
| The two major mRNA decay pathways in euks are initiated by... |
|
Definition
| deandenylation catalyzed by poly(A) nucleases |
|
|
Term
| The deadenylation step in eukaryotic mRNA degrradation may be followed either by... or... |
|
Definition
| decapping and 5' to 3' exonuclease digestion or by 3' to 5' exonuclease digestion |
|
|
Term
| The decapping enzyme competes with... for 5' cap binding |
|
Definition
| the translation initiation complex |
|
|
Term
| The ____, which catalyzes 3' to 5' mRNA digestion, is a large, evolutionarily conserved complex |
|
Definition
|
|
Term
| Degradation (euks) may occur within discrete cytoplasmic particles called... |
|
Definition
|
|
Term
|
Definition
| oocyte particles containing translationally repressed mRNAs awaiting activation later in development |
|
|
Term
|
Definition
| particles containing translationally repressed mRNAs in transit to final cell destinations |
|
|
Term
|
Definition
| cytoplasmic particles, containing translationally inactive mRNAs, that form in response to a general inhibition of translation initiation |
|
|
Term
| The degradation of the nonpolyadenylated histone mRNAs is initiated by... |
|
Definition
| 3' addition of a poly(U) tail |
|
|
Term
| Degradation of some mRNAs may be initiated by... |
|
Definition
| sequence-specific or structure-specific endonucleolytic cleavage |
|
|
Term
| An unknown number of mRNAs are target for degradation or translational repression by... |
|
Definition
|
|
Term
| iron-response element (IRE) |
|
Definition
| a cis sequence found in certain mRNAs whose stability or translation is regulated by cellular iron concentration |
|
|
Term
| Aberrant nuclear RNAs are identified and destroyed by... |
|
Definition
| an RNA surveillance system |
|
|
Term
| The nuclear exosome functions both in the... |
|
Definition
| processing of normal substrate RNAs and in the destruction of aberrant RNAs |
|
|
Term
| The yeast ____ complex recruits the exosome to aberrant RNAs and facilitates its 3' to 5' exonuclease activity |
|
Definition
|
|
Term
|
Definition
| a short poly(A) tail (less than 15 A) |
|
|
Term
| Substrates for TRAMP-exosome degradation include... |
|
Definition
| unspliced or aberrantly spliced pre-mRNAs and improperly terminated RNA pol II transcripts lacking a poly(A) tail |
|
|
Term
| Localization of mRNAs serves diverse functions in... |
|
Definition
| single cells and developing embryos |
|
|
Term
| How many mechanisms for the localization of mRNA have been documented? |
|
Definition
|
|
Term
| In the localization of Ash1 mRNA, starting from the RNA and ending at the actin filament, describe the structure |
|
Definition
She2 binds stem-loops in mRNA
She3 connects She2 to myosin
Myo4 binds to actin filament |
|
|
Term
| Localization requires.... |
|
Definition
| cis elements on the target mRNA and trans factors to mediate localization |
|
|
Term
|
Definition
| any of the number of RNA cis elements involved in directing cellular localization |
|
|
Term
| The predominant active transport mechanism involves the directed movement of... |
|
Definition
| mRNPs along cytoskeletal tracks |
|
|
Term
|
Definition
| transposon that codes for the enzymes needed for transposition flanked by short inverted terminal repeats |
|
|
Term
| The target site at which a transposon is inserted is.... |
|
Definition
| duplicated during the insertion process to form two repeats in direct orientation at the ends of the transposon (direct repeats) |
|
|
Term
| The length of the direct repeat is... |
|
Definition
|
|
Term
|
Definition
| the enzyme activity involved in insertion of a transposon at a new site |
|
|
Term
|
Definition
| other genes in addition to those coding for transposition |
|
|
Term
| composite elements/transposons |
|
Definition
| have a central region flanked by an IS at each end |
|
|
Term
| The order of events and exact nature of the connections between transposon and target DNA determine whether the transposition is... |
|
Definition
| replicative or nonreplicative |
|
|
Term
| Difference between replicative and nonreplicative transposition? |
|
Definition
Replicative = copy of transposon created
Non = transposon moves from donor to recepient |
|
|
Term
| Homologous recombination between the repeats of a transposon may lead to... |
|
Definition
| precise or imprecise excision |
|
|
Term
| An integrated provirus is a... |
|
Definition
| double stranded DNA sequence |
|
|
Term
|
Definition
| an enzyme responsible for a site-specific recombination that inserts one molecule of DNA into another |
|
|
Term
| A typical retrovirus has the following 3 genes... |
|
Definition
|
|
Term
| Gag and Pol proteins are translated from... |
|
Definition
| a full-length transcript of the genome |
|
|
Term
| Translation of Pol requires a... |
|
Definition
| readthrough or a frameshift by the ribosome |
|
|
Term
| Env is translated from a... |
|
Definition
| separate mRNA that is generated by splicing |
|
|
Term
|
Definition
| a virus with a single-stranded nucleic acid genome whose sequence directly codes for the protein products |
|
|
Term
| replication-defective virus |
|
Definition
| a virus that cannot perpetuate an infective cycle because some of the necessary genes are absent or mutated |
|
|
Term
|
Definition
| Long interspersed elements--a major class of retroposons that occupy ~21% of the human genome |
|
|
Term
|
Definition
| Short interspersed elements--a major class of short (<500bp) nonautonomous retrotransposons that occupy ~13% of the human genome |
|
|
Term
|
Definition
| one of a set of dispersed, related sequences, each ~300 bp long, in the human genome (members of the SINE family) |
|
|
Term
| Transposons and retroposons constitute... |
|
Definition
| almost half of the human genome |
|
|
Term
| RNA functions as a regulator by... |
|
Definition
| forming a region of secondary structure (either inter- or intramolecular) that changes the properties of a target sequence |
|
|
Term
|
Definition
| a gene that has a complementary sequence to an RNA that is its target |
|
|
Term
|
Definition
| RNA that has a complementary sequence to an RNA that is its target |
|
|
Term
| Eukaryotic genomes code for many short (~22 bp) RNA molecules called... |
|
Definition
|
|
Term
|
Definition
| a process by which short 21-23 NT antisense RNAs, derived from longer double-stranded RNAs, can modulate expression of mRNA by translation inhibition or degradation |
|
|
Term
|
Definition
| short temporal RNA, a form of miRNA in euks that modulates mRNA expression during development |
|
|
Term
|
Definition
| regulate gene expression in germ cells and act to silence transposable elements |
|
|
Term
|
Definition
| complementary to viruses and transposable elements |
|
|
Term
|
Definition
| an endonuclease that processes double-stranded primary RNAs into short, ~70 bp precursors for Dicer processing |
|
|
Term
|
Definition
| an endonuclease that processes double stranded precursor RNA to 21-23 NT molecules |
|
|
Term
|
Definition
| RNA-induced silencing complex, a ribonucleoprotein particle composed of a short single stranded siRNA and a nuclease that may cleave mRNAs complementary to the siRNA |
|
|
Term
|
Definition
| a germline subset of miRNA transcribed from transposable elements and other repeated elements that is used to silence transposable elements |
|
|
Term
| MicroRNAs regulate gene expression by... |
|
Definition
| base pairing with complementary sequences in target mRNAs |
|
|
Term
| RNA interference triggers ____ or ____ of mRNAs complementary to miRNA or siRNA |
|
Definition
| degradation or translation inhibition |
|
|
Term
|
Definition
1) Dicer cleaves to siRNA
2) Argonaute and additional proteins come in, forming RISC
3) Interference occurs |
|
|
