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Fundamentals I Test 3 Ryan
Flash Cards for Dental School
124
Biochemistry
Professional
09/15/2010

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Term
What is the compact structure formed by the prokaryotic genome?
Definition
Nucleoid
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
True
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
Growth Rate
Term
The unstable half-life of mRNA allows regulation at what level?
Definition
mRNA synthesis
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?
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
Alpha
Term
Which RNA polymerase subunit binds NTPs, interacts with σ, and forms catalytic site with β'?
Definition
Beta
Term
Which RNA polymerase subunit binds DNA and forms catalytic site with β?
Definition
Beta Prime
Term
Which RNA polyermase subunit recognizes promoter sequences on DNA and aids in melting dsDNA?
Definition
Sigma
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
Second
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
Rifamycin (rifampicin)
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
Topoisomerase
Term
What consists of 60bp RNAP core with 17 bp unwound?
Definition
Transcription Bubble
Term
What must the transcription bubble contact for polymerization?
Definition
The active site
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
DNA Termination Site
Term
Is "Intrinsic Termination" factor independent or factor dependent?
Definition
Factor Independent
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
Promoter
Term
What is a region of DNA containing signals for termination of transcription?
Definition
Terminator
Term
What is DNA that encodes a protein?
Definition
Structural Gene
Term
What is mRNA specified by the structural gene?
Definition
cistron
Term
What is structural gene or cistron?
Definition
Coding Region
Term
What is a coding region without stop codons?
Definition
Open Reading Frame
Term
What is a promoter + gene(s) + terminator?
Definition
Operon
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
Repressor
Term
What is a DNA binding protein that increases the efficiency of transcription at the promoter?
Definition
Activator
Term
What is the primary site of control in prokaryotes?
Definition
Transcription
Term
What is defined as a regulatory sequence adjacent to an operon that determines whether it is transcribed?
Definition
Operator
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
Operon
Term
What is described as a set of genes expressed from separate promoter sites but controlled by the same regulatory molecule?
Definition
Regulon
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
lac repressor
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
lacZ
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
lac repressor
Term
What co-repressor binds lac repressor & induces a cooperative allosteric change?
Definition
β-galactosides
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
No Glucose, Yes Lactose
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
RNA polymerase
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
Eukaryotes
Term
What percent of the human genome encodes for protein?
Definition
1.5%
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
Heterochromatin
Term
What is the fundamental unit of organization of the chromatin fiber?  What are its basic proteins?
Definition
Nucleosome; Histones
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
True
Term
What happens to chromatin structure when the histone tails are acetylated?
Definition
becomes more extended and open
Term
Are scaffold proteins histones?
Definition
No
Term
What is formed by DNA wound around histone octamers?
Definition
Nucleosome
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
TFIID
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
RNA Pol I
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
5S rRNA
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
TFIID
Term
Which RNA Pol II Transcription Factor facilitates & stabilizes binding of TFIID complex?
Definition
TFIIA
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
TFIIH, helicase activity
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
position -25
Term
Is the TATA box on the coding or non-coding strand?
Definition
Non-coding
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
Metallothionein
Term
What stimulates Cytoplasmic Glucocorticoid to move into nucleus & affect gene transcription?
Definition
Cortisol
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
Enhancers; Silencer
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
Yes
Term
T/F Histone Acetyl Transferases open Chromatin to be transcribed.
Definition
True; HAT
Term
What process is responsible for reprograming diploid somatic cell nucleus to recapitulate development?
Definition
Chromatin remodeling
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