Term
| What is the compact structure formed by the prokaryotic genome? |
|
Definition
|
|
Term
| What are the 3 major types of RNA? |
|
Definition
| Messenger mRNA, Ribosomal rRNA, Transfer tRNA |
|
|
Term
| How many DNA dependent RNA polymerases are used in prokaryotes? Eukaryotes? |
|
Definition
| One (ie. archea & eubacteria); Three (I, II, & III) |
|
|
Term
| T/F rRNA and tRNA are Not degraded rapidly and are extensively processed. |
|
Definition
|
|
Term
| In E. coli what percent of RNA is rRNA? tRNA? mRNA? |
|
Definition
| 80% rRNA, 15% tRNA, 2-5% mRNA |
|
|
Term
| What is Ribosome number [rRNA] proportional to? |
|
Definition
|
|
Term
| The unstable half-life of mRNA allows regulation at what level? |
|
Definition
|
|
Term
| In what type of organisms do you find Exonucleases? Where in the genome do they act? |
|
Definition
| Bacteria; 3' - 5' end of genome |
|
|
Term
| Where in the genome do Endonucleases act? |
|
Definition
| In the middle of the mRNA |
|
|
Term
| What are the four "Playas" in Transcription? |
|
Definition
| Ribonucleotides (NTPs), Template (DNA), DNA Dependent RNA Polymerase, & Transcription Factors |
|
|
Term
| In Transcription, in what direction is the DNA template strand read? In what direction does the mRNA transcript grow? |
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Definition
| Template read 3' to 5'; Transcript grows 5' to 3' |
|
|
Term
| What four bases are found in DNA? How do these differ in RNA? |
|
Definition
DNA: Adenine, Cytosine, Guanine, Thymine
RNA: Uracil instead of Thymine |
|
|
Term
| In what direction does DNA Dependent RNA Polymerase catalyze synthesis? Does it require a primer? Does it require a template? |
|
Definition
| 5' to 3'; No primer required, Template required |
|
|
Term
| What are the four major differences between DNA & RNA? |
|
Definition
1. Deoxyribose vs. Ribose
2. Thymine vs. Uracil
3. RNA is Single Stranded
4. RNA is complementary to one strand of DNA |
|
|
Term
| What are the subunits that make up the Prokaryotic RNA polymerase Holoenzyme? What subunits make up the Core Enzyme? What does each one do? |
|
Definition
Holoenzyme: α2ββ'σ - initiates RNA synthesis at a promoter
Core Enzyme: α2ββ' - elongation of RNA chain |
|
|
Term
| Which RNA polymerase subunit is essential for assembly & activation of enzyme? |
|
Definition
|
|
Term
| Which RNA polymerase subunit binds NTPs, interacts with σ, and forms catalytic site with β'? |
|
Definition
|
|
Term
| Which RNA polymerase subunit binds DNA and forms catalytic site with β? |
|
Definition
|
|
Term
| Which RNA polyermase subunit recognizes promoter sequences on DNA and aids in melting dsDNA? |
|
Definition
|
|
Term
| What two major events occur in Initiation of Transcription? |
|
Definition
1. Holoenzyme binds promoter, unwinds DNA, & forms phosphodiester bonds
2. Need σ to recognize promoter |
|
|
Term
| What two major events occur in Elongation of Transcription? |
|
Definition
1. σ dissociates
2. Core enzyme elongates RNA w/high processivity |
|
|
Term
| What two major events occur in Termination of Transcription? |
|
Definition
1. Polymerase dissociates from template DNA & releases new RNA
2. Rho(ρ)-factor dependent or independent |
|
|
Term
| Describe the process of RNA Polymerase finding the promoter on DNA. |
|
Definition
| Polymerase binds nonspecifically to DNA (low affinity), Sigma subunit recognizes promoter, Holoenzyme & promoter form "closed promoter complex", polymerase unwinds 14 base pairs to form "open promoter complex" |
|
|
Term
| How does the Holoenzyme search for promoters? |
|
Definition
| Slides along the DNA via intramolecular transfer on the chromosome |
|
|
Term
| How many base pairs do promoter contain & on which side of the start site are they found? |
|
Definition
| 40bp; on the 5'-side of start site |
|
|
Term
| What are the two consensus sequence elements? |
|
Definition
1. "-35 region" (TTGACA)
2. Pribnow box near -10 (TATAAT) - ideal for unwinding |
|
|
Term
| T/F The sigma factor is only present in the closed form. |
|
Definition
| False, sigma factor is present in the closed & open form |
|
|
Term
| What number is assigned to the transcription start site? Is upstream in the positive or negative direction? |
|
Definition
| Transcription Start Site = +1; Upstream = Negative |
|
|
Term
| What does the Initiation site prefer to bind to? |
|
Definition
| ATP and GTP (most RNAs begin with a purine at the 5'-end) |
|
|
Term
| Does the Elongation site bind the first or second incoming NTP? |
|
Definition
|
|
Term
| How are phosphoester bonds formed? |
|
Definition
| 3'-OH of first NTP attacks alpha-P of second NTP |
|
|
Term
| When is Initiation Complete? |
|
Definition
| When 7-12 unit oligonucleotide is made & sigma subunit dissociates |
|
|
Term
| What medication binds Beta subunit of prokaryotic RNA polymerase & blocks first phosphodiester bond? |
|
Definition
|
|
Term
| What is the typical rate of Elongation? Is Elongation slower in G/C or A/T rich regions? |
|
Definition
| 20-50 bp/sec; G/C-rich regions are slower |
|
|
Term
| What precedes and follows polymerase to relieve supercoiling? |
|
Definition
|
|
Term
| What consists of 60bp RNAP core with 17 bp unwound? |
|
Definition
|
|
Term
| What must the transcription bubble contact for polymerization? |
|
Definition
|
|
Term
| Name two inhibitors of Transcription and whether they function in Prokaryotes or Eukaryotes? |
|
Definition
Actinomycin D (pro & eukaryotes)
Rifampicin/Rifampin (prokaryotes) |
|
|
Term
| What ist the Termination factor and what kind of enzyme is it? |
|
Definition
| Rho; ATP-dependent helicase |
|
|
Term
| What is characterized by inverted repeats rich in G:C which form a stem-loop in the RNA transcript? |
|
Definition
|
|
Term
| Is "Intrinsic Termination" factor independent or factor dependent? |
|
Definition
|
|
Term
| At what levels does Prokaryotic Regulation occur? |
|
Definition
| Transcription (RNA synthesis); RNA stability, processing, localization; Translation; and Post-translation |
|
|
Term
| What is a DNA site recognized by RNA polymerase for specific transcriptional initiation? |
|
Definition
|
|
Term
| What is a region of DNA containing signals for termination of transcription? |
|
Definition
|
|
Term
| What is DNA that encodes a protein? |
|
Definition
|
|
Term
| What is mRNA specified by the structural gene? |
|
Definition
|
|
Term
| What is structural gene or cistron? |
|
Definition
|
|
Term
| What is a coding region without stop codons? |
|
Definition
|
|
Term
| What is a promoter + gene(s) + terminator? |
|
Definition
|
|
Term
| What is the 3D structure of regulatory proteins and what type of DNA sequence do they recognize? |
|
Definition
| Homodimers; Palindromic (have dyad symmetry) |
|
|
Term
| What is a DNA binding protein that decreases the efficiency of transcription at the promoter? |
|
Definition
|
|
Term
| What is a DNA binding protein that increases the efficiency of transcription at the promoter? |
|
Definition
|
|
Term
| What is the primary site of control in prokaryotes? |
|
Definition
|
|
Term
| What is defined as a regulatory sequence adjacent to an operon that determines whether it is transcribed? |
|
Definition
|
|
Term
| What does the binding of regulatory proteins to the operator influence to affect transcription rate? |
|
Definition
| access of RNA polymerase to promoter |
|
|
Term
| What is described as a set of genes that are transcribed from the same promoter & controlled by the same operator site & regulatory proteins? |
|
Definition
|
|
Term
| What is described as a set of genes expressed from separate promoter sites but controlled by the same regulatory molecule? |
|
Definition
|
|
Term
| What are the metabolites of induction called? Of repression? |
|
Definition
| co-inducers; co-repressors |
|
|
Term
| What substrates induce enzyme synthesis even though the enzymes can't metabolize the substrate? Give an example. |
|
Definition
| Gratuitous Inducers - IPTG |
|
|
Term
| Is lacI gene the lac repressor or inducer? How do lacI mutant genes express genes needed for lactose metabolism? |
|
Definition
| Repressor; Constitutively |
|
|
Term
| What forms a tetramer with DNA binding in the N-terminal domain & Inucer binding at the C-terminal domain? |
|
Definition
|
|
Term
| What is the lac operons normal state (off or on)? When does it change? |
|
Definition
| Normally off; only fully on when lactose is present & glucose is absent |
|
|
Term
| Are genes under lac Operon control transcribed in the presence of lactose? |
|
Definition
| Yes, when lactose is present the lac repressor is removed; when lactose is absent transcription is inhibited |
|
|
Term
| What enzyme catalyzes hydrolysis of linkage between lactose to form two galactose? |
|
Definition
|
|
Term
| Describe the operator site. (what kind of code is it? is it upstream or downstream from transcription initiation site?) |
|
Definition
| it's Palindromic & lies downstream from transcription initiation site |
|
|
Term
| What is a tetrameric molecule that blocks transcription elongation by RNAP? |
|
Definition
|
|
Term
| What co-repressor binds lac repressor & induces a cooperative allosteric change? |
|
Definition
|
|
Term
| Is the expression of glucose-sensitive operons reduced or enhanced in the presence of glucose? What is this effect called? |
|
Definition
| Reduced; Catabolite Repression |
|
|
Term
| Describe CAP. (What does it stand for, what is its structure, how does it act, what is its function?) |
|
Definition
| Catabolite Activator Protein; homodimer; N-term bind cAMP & C-term binds DNA causing DNA to bend; Assists formation of closed promoter complex called CRP (cAMP Receptor Protein) |
|
|
Term
| Describe the activation of CAP during Glucose starvation. |
|
Definition
| low Glucose triggers adenylyl cyclase - cAMP levels increase - cAMP is a co-inducer to CAP - CAP-cAMP binds upstream from promoter & activates transcription |
|
|
Term
| Under what glucose & lactose condition is the Operon turned On? |
|
Definition
|
|
Term
| What kind of control does trp Operon exhibit? What is it's normal state & how is that changed? (off or on) |
|
Definition
| Co-repressor Mediated Negative Control - Autogenous Regulation; Always On unless tryptophan levels are high enough to turn off (Tryptophan = co-repressor) |
|
|
Term
| What does the binding of trp repressor exclude from the promoter site? |
|
Definition
|
|
Term
| If a ribosome "stalls" on the trp codon does transcription of the trp Operon proceed or terminate? What if the ribosome passes quickly? |
|
Definition
Stall: Proceeds
Quickly: Terminates |
|
|
Term
| Are pre-mRNAs of eukaryotes or prokaryotes subject to extensive post-transcriptional modification? |
|
Definition
|
|
Term
| What percent of the human genome encodes for protein? |
|
Definition
|
|
Term
| What are the two types of repeat elements in human genome? |
|
Definition
| LINES (Long Interspersed Nuclear Elements) & SINES (Short) |
|
|
Term
| Nucleoprotein material of eukaryotic chromosome is called___? |
|
Definition
| Chromatin; complex of DNA, protein, & RNA |
|
|
Term
| Which type of DNA is accessible for transcription? Which type is inactive? Which type is most numerous? |
|
Definition
| Euchromatin = accessible; Heterochromatin = inactive; Mostly Euchromatin |
|
|
Term
| Which type of DNA is found at centromeres & telomeres? |
|
Definition
|
|
Term
| What is the fundamental unit of organization of the chromatin fiber? What are its basic proteins? |
|
Definition
|
|
Term
| What are the two most common AA's in Histones, why? |
|
Definition
| Lysine & Arginine b/c they have a positive charge that attracts DNA |
|
|
Term
| Which histones are part of the octet? In the octet which histones form dimers? What does the other one do? |
|
Definition
| H2A, H2B, H3, & H4 form the octet; H2A & H2B = dimer and H3 & H4 = dimer; H1 associates w/neighboring nucleosomes to form a 30 nm solenoid |
|
|
Term
| T/F Histones are among the most highly conserved eukaryotic proteins. |
|
Definition
|
|
Term
| What happens to chromatin structure when the histone tails are acetylated? |
|
Definition
| becomes more extended and open |
|
|
Term
| Are scaffold proteins histones? |
|
Definition
|
|
Term
| What is formed by DNA wound around histone octamers? |
|
Definition
|
|
Term
| Which RNA Polymerase is most sensitive to α-amanitin? Rank the others. |
|
Definition
| RNA Polymerase II >> Pol III >> Pol I |
|
|
Term
| Via what kinds of interactions doe RNA polymerases interact with their promoters? |
|
Definition
| Protein:Protein and Protein:DNA |
|
|
Term
| What are the three major structures in Transcription Factors? |
|
Definition
| 1. Helix-Turn-Helix 2. Zinc-Finger (can correct or mutate genes) 3. Leucine Zipper (bZIP) |
|
|
Term
| What positions RNAPs at transcription initiation sites forming preinitiation complex? |
|
Definition
| General Trancription Factors (GTFs) |
|
|
Term
| What are the components of the Transcription-Initiation Complex? |
|
Definition
| RNAP + GTF bound to promoter region |
|
|
Term
| Which GTF is the largest & cosists of TATA-box binding protein and 8-10 TBP-associated factors? |
|
Definition
|
|
Term
| What is the "universal transcription factor"? Which RNAPs does it associate with? Does it associate with promoters with or without a TATA box? |
|
Definition
| TBP; All three RNAPs; With or Without TATA box |
|
|
Term
| What are the two roles of TFIID? |
|
Definition
1. foundation of transcriptional PIC complex
2. prevent nucleosome stabilization in promoter region (H1 antagonist) |
|
|
Term
| Which RNA Pol transcribes genes for the large rRNA precursor? |
|
Definition
|
|
Term
| What does RNAP III transcribe? |
|
Definition
| small RNAs: 5S rRNA, tRNA precursors, U6 snRNA |
|
|
Term
| What small RNA's promoter is entirely within the coding region of the gene? |
|
Definition
|
|
Term
| Where are Class II promoters located? |
|
Definition
| completely inside the promoter region |
|
|
Term
| What are TBP-associated Factors important for? |
|
Definition
| helping TBP bind promoters that lack TATA boxes |
|
|
Term
| Which RNA Pol II Transcription Factor binds TATA box via TBP subunit? |
|
Definition
|
|
Term
| Which RNA Pol II Transcription Factor facilitates & stabilizes binding of TFIID complex? |
|
Definition
|
|
Term
| What happens at the C & N termini of the TFIIB monomer? |
|
Definition
C: contacts DNA & TBP
N: extends toward start site |
|
|
Term
| Which RNA Pol II Transcription Factor unwinds DNA downstream from initiator site in presence of ATP? |
|
Definition
|
|
Term
| TFIIH, helicase activityWhat is described as a stretch of 7 aa's that repeat multiple times and is critical for viability? |
|
Definition
| Carboxyl-Terminal Domain (CTD Tail) |
|
|
Term
| What are the two parts of the RNA Pol II Promoters? |
|
Definition
1. Core promoter (TATA box & initiator)
2. Proximal Promoter Elements (upstream, downstream, or internal) |
|
|
Term
| Where is the TATA motif usually located? |
|
Definition
|
|
Term
| Is the TATA box on the coding or non-coding strand? |
|
Definition
|
|
Term
| What determines whether RNA will be transcribed? |
|
Definition
| Sum total of all transcription factors |
|
|
Term
| What is a responsive element? For what do they act as binding sites? |
|
Definition
| DNA sequence located in cis position on repsonsive genes. Binding sites for Transacting Factors |
|
|
Term
| What binds metals such as Cadmium to get rid of them? (It can also be triggered by stress.) |
|
Definition
|
|
Term
| What stimulates Cytoplasmic Glucocorticoid to move into nucleus & affect gene transcription? |
|
Definition
|
|
Term
| What are the 7 modes of activation of Transacting Factors? |
|
Definition
| Protein Synthesis, Ligand Binding, Protein Phosphorylation, Addition of Second Subunit, Unmasking, Stimulation of Nuclear Entry, and Release from Membrane |
|
|
Term
| What is a control element that stimulates transcription? What is it called if it is negative? |
|
Definition
|
|
Term
| Where do Enhancers occur? Are they orientation dependent? Are they Cell-type specific? |
|
Definition
| upstream, downstrea, in introns, & exons; orientation independent; may be cell-type specific |
|
|
Term
| What initiates activation of transcription in eukaryotes? |
|
Definition
| Recruitment of RNA pol II holoenzyme complex |
|
|
Term
| What blocks encroachment of heterochromatic from neighboring loci & stop unregulated enhancement of neighborin genes? |
|
Definition
| Boundary Elements or Insulators |
|
|
Term
| Is DNA active or silenced when Hypomethylated? |
|
Definition
| Hypomethylation = Active; Hypermethylation = Silenced |
|
|
Term
| What removes acetyl groups from histones resulting in gene silencing? |
|
Definition
| Histone Deacetylase (HDAC) |
|
|
Term
| What are the four postranslational modifications of Histone tails? |
|
Definition
| Acetylation, Methylation, Phosphorylation & Ubiquitination |
|
|
Term
| Does Chromatin Remodeling require ATP? |
|
Definition
|
|
Term
| T/F Histone Acetyl Transferases open Chromatin to be transcribed. |
|
Definition
|
|
Term
| What process is responsible for reprograming diploid somatic cell nucleus to recapitulate development? |
|
Definition
|
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