Exam 2 (Everything) Flashcards
What is the major control point of transcription?
Initiation
In lambda phage, the Q cut site overlaps:
Promoter to the right ‘
What group of genes is transcribed by PR’
Late genes
Which lambda phage promoter is autoregulated by the lambda repressor?
The promoter of repressor maintenance (PRM)
Which lambda phage promoter is used to transcribe an antisense product of cro and the lambda repressor?
The promoter of repressor establishment (PRE)
If lambda phage had a mutation in OR3 in both the promoter to the right and the promoter to the left that reduced the affinity for cro, would this promote lysis or lysogeny?
Lysogeny
If lambda phage infects E. coli cells that are expressing genes of the lac operon, will lambda most likely choose to undergo lysis or lysogeny?
Lysogeny
Which part of RNA polymerase II moves the most during transcription?
Clamp
Which eukaryotic RNA polymerase transcribes the tRNA genes?
RNA polymerase III
Which eukaryotic RNA polymerase transcribes the rRNA genes?
RNA polymerase I
Which eukaryotic RNA polymerase transcribes the mRNA genes?
RNA polymerase II
When RNA polymerase II is said to be “processive”, what does this mean?
The enzyme forms a stable interaction with the template and will transcribe until it reaches a terminator
Which region of RNA polymerase II positions the template strand of the DNA to be transcribed and then translocates it during synthesis?
The bridge helix
Which region of RNA polymerase II maintains the dissociation of the RNA-DNA hybrid during transcription elongation?
The lid
Which region of RNA polymerase II contains the zipper, rudder and lid?
The clamp
Which region of RNA polymerase II initiates the dissociation of the template DNA?
The zipper
Which region of the RNA polymerase II enzyme initiates the dissociation of the RNA-DNA hybrid?
The rudder
When RNA polymerase II is transcribing a gene, where is the upstream DNA relative to the downstream DNA?
Perpendicular to it
Which transcription factor does NOT cause DNA to bend when it binds DNA?
Zif286 (TBP and CAP do bend DNA)
Which one of the general transcription factors in most like the sigma subunit of E. coli RNA polymerase?
TFIIF
What happens after the carboxy terminal domain of the large subunit of RNA polymerase II has been phosphorylated by TFIIH?
The polymerase begins elongation
What are the three most common types of transcription activation domains within gene specific transcription factors?
Acidic, glutamine rich, and proline rich
What are the 3 eukaryotic helix turn helix proteins?
The homeodomain proteins: Antennapedia, engrailed, Mat a-2
What are the 2 prokaryotic helix turn helix proteins?
The lambda repressor proteins: cro and CAP
Normally, the thyroid hormone receptor is a repressor and the estrogen receptor is an activator. If you exchanged the repressive and activation domains between these two proteins, what would happen if you added thyroid hormone to cells expressing both of the new fusion proteins (but not the wild type proteins)?
Thyroid hormone receptor target genes would be activated
Normally, the thyroid hormone receptor is a transcriptional repressor and the estrogen receptor is a transcriptional activator. If you exchange the ligand binding domains between these two proteins, what would happen if you added thyroid hormone to cells expressing both of the new fusion proteins (but not the wild type proteins)?
Thyroid hormone receptor target genes would be activated
Normally, the thyroid hormone receptor is a repressor and the estrogen receptor is a activator. If you exchange the DNA binding domains between these two proteins, what would happen if you added thyroid hormone to cells expressing both of the new fusion genes (but not the wild type proteins)?
Estrogen receptor target genes would be repressed
Which family of transcription factors bind both the major groove and minor groove?
Helix-turn-helix
Which family of transcription factors bind to two successive major grooves in DNA?
Zinc finger
In DNA sequencing by the Sanger dideoxy chain termination approach, the DNA strand whose sequence is directly determined (i.e. read from autoradiographs of sequencing gels) is the strand that:
Has the same sequence as the primer
In which two sequencing methods are chain-terminating nucleotides required for DNA sequencing?
Sanger and Illumina
In a single well of a pico titer plate is a single bead with 1 million single-stranded DNA molecules attached. Each molecule contains 220 nucleotides of genomic DNA. What is the maximum base pairs of DNA sequence information that can be obtained from this one well?
220 base pairs
What method requires an amplification step prior to sequencing?
Illumina
What are promoters?
Specific RNA polymerase binding sites on DNA
What is the difference between the RNA polymerase core and the RNA polymerase holoenzyme?
The holoenzyme binds promoters more tightly than the core enzyme because of the sigma factor
Which subunit of RNA polymerase binds to the -35 and -10 boxes of prokaryotic promoters?
Sigma
When are the genes within the lac operon induced?
In the presence of low concentrations of glucose
Which of the following subunits of prokaryotic RNA polymerase bind to UP elements within promoters?
Alpha
In lambda phage, what is the function of N?
It is an antiterminator protein that binds to its own transcript
In the forensic use of DNA for identification of individuals using PCR and VNTR minisatellite DNA, PCR primers must be complementary to:
Unique DNA sequences not included in the variable number tandem repeats
What mechanism do transposons move by?
Cut and paste
What mechanism do retrotransposons move by?
Copy and paste
Consider a 5 bp tandemly-repeated micro satellite DNA found in three arrays scattered throughout the genome. One array has 50 tandem repeats. One array has 1000 tandem repeats. One array has 500 tandem repeats. What is the copy number of the repeat?
1550
Genes that are transcribed but not translated into protein are classified as:
RNA-coding genes
Experiments in which isolated nuclei are treated with micrococcal nuclease provide evidence for:
The existence of nucleosomes
In vertebrate animals and plants, the nucleosome core is made up of:
8 histones and 146 bp of DNA
In a transformation experiment, two foreign genes were introduced into the genome of plant cells in culture, GFP (Green Fluorescent Protein) and NPTII (neomycin phosphotransferase), a gene whose protein product inactivates the antibiotic neomycin. Which is the screenable marker and which is the selectable marker?
GFP = screenable NPTII = selectable
The genome of a certain bird found in the Galapagos Islands has a genome size of 2 Gbp. In a genome reassociation experiment, one-fourth of the genome was found to reassociate as a class of repetitive DNA sequences with a Cot1/2 of 2 x 10-2 moles bp x sec x l-1. Under the same conditions of stringency, E. coli DNA with a complexity of 4.2 x 106 bp has a Cot1/2 of 8.4 moles bp x sec x l-1. What is the complexity of this class of repetitive sequences in the Galapagos Island bird?
1 x 10^4 bp
The genome of the phage T4 contains 1.7 x 105 base pairs. The genome of E. coli contains 4.2 x 106 base pairs. In both cases the genomes are simple-sequence DNA, i.e., they contain all unique sequences, no repetitive DNA. Which genome has the greater complexity?
E.coli
What is the function of RAP30?
Mediates binding of TFIIF to the core
Which part of helix-turn-helix domains bind in the major groove, and which part binds in the minor groove on the opposite side?
Major: recognition helix
Minor: N-terminus
What is the most common DNA binding motif?
2 hydrogen bonds formed between Arginine side chain of the transcription factor and the guanine base of DNA
How do hormone receptors bind DNA?
As a dimer on one face of the DNA double helix, with each subunit in successive major grooves
Which groove of the DNA do TBP’s bind?
The minor groove; forcing open the DNA
What are 2 of the main functions of Rpb4/7?
Locks clamp in closed formation and provides a binding surface for RNA exiting the elongating polymerase
GTPase Ras
Dominant-negative; bind GDP and stay in inactive state
What is the function of the CTD?
Binds proteins involved in capping, splicing, and polyadenylating precursor mRNAs
Genes O & P
Code for the proteins needed for phage DNA replication
How does PRE help to promote lysogeny?
It direct transcription leftward through cro & cl, producing antisense product of cro (since cro is usually transcribed rightward from PR)
Where is PRE located?
To the right of PR and cro
What is the consensus bind sequence of bHLH proteins?
5’-CANNTG-3’
When can a lysogen enter lytic phase?
When it encounters mutagenic chemicals, UV light, or radiation
What is meant by “processive”?
Antitermination factors remain associated with polymerase as it moves down the DNA
