Exam 2 (Everything)

Question 1

What is the major control point of transcription?

Answer 1

Initiation

Question 2

In lambda phage, the Q cut site overlaps:

Answer 2

Promoter to the right ‘

Question 3

What group of genes is transcribed by PR’

Answer 3

Late genes

Question 4

Which lambda phage promoter is autoregulated by the lambda repressor?

Answer 4

The promoter of repressor maintenance (PRM)

Question 5

Which lambda phage promoter is used to transcribe an antisense product of cro and the lambda repressor?

Answer 5

The promoter of repressor establishment (PRE)

Question 6

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?

Answer 6

Lysogeny

Question 7

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?

Answer 7

Lysogeny

Question 8

Which part of RNA polymerase II moves the most during transcription?

Answer 8

Clamp

Question 9

Which eukaryotic RNA polymerase transcribes the tRNA genes?

Answer 9

RNA polymerase III

Question 10

Which eukaryotic RNA polymerase transcribes the rRNA genes?

Answer 10

RNA polymerase I

Question 11

Which eukaryotic RNA polymerase transcribes the mRNA genes?

Answer 11

RNA polymerase II

Question 12

When RNA polymerase II is said to be “processive”, what does this mean?

Answer 12

The enzyme forms a stable interaction with the template and will transcribe until it reaches a terminator

Question 13

Which region of RNA polymerase II positions the template strand of the DNA to be transcribed and then translocates it during synthesis?

Answer 13

The bridge helix

Question 14

Which region of RNA polymerase II maintains the dissociation of the RNA-DNA hybrid during transcription elongation?

Answer 14

The lid

Question 15

Which region of RNA polymerase II contains the zipper, rudder and lid?

Answer 15

The clamp

Question 16

Which region of RNA polymerase II initiates the dissociation of the template DNA?

Answer 16

The zipper

Question 17

Which region of the RNA polymerase II enzyme initiates the dissociation of the RNA-DNA hybrid?

Answer 17

The rudder

Question 18

When RNA polymerase II is transcribing a gene, where is the upstream DNA relative to the downstream DNA?

Answer 18

Perpendicular to it

Question 19

Which transcription factor does NOT cause DNA to bend when it binds DNA?

Answer 19

Zif286 (TBP and CAP do bend DNA)

Question 20

Which one of the general transcription factors in most like the sigma subunit of E. coli RNA polymerase?

Answer 20

TFIIF

Question 21

What happens after the carboxy terminal domain of the large subunit of RNA polymerase II has been phosphorylated by TFIIH?

Answer 21

The polymerase begins elongation

Question 22

What are the three most common types of transcription activation domains within gene specific transcription factors?

Answer 22

Acidic, glutamine rich, and proline rich

Question 23

What are the 3 eukaryotic helix turn helix proteins?

Answer 23

The homeodomain proteins: Antennapedia, engrailed, Mat a-2

Question 24

What are the 2 prokaryotic helix turn helix proteins?

Answer 24

The lambda repressor proteins: cro and CAP

Question 25

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)?

Answer 25

Thyroid hormone receptor target genes would be activated

Question 26

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)?

Answer 26

Thyroid hormone receptor target genes would be activated

Question 27

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)?

Answer 27

Estrogen receptor target genes would be repressed

Question 28

Which family of transcription factors bind both the major groove and minor groove?

Answer 28

Helix-turn-helix

Question 29

Which family of transcription factors bind to two successive major grooves in DNA?

Answer 29

Zinc finger

Question 30

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:

Answer 30

Has the same sequence as the primer

Question 31

In which two sequencing methods are chain-terminating nucleotides required for DNA sequencing?

Answer 31

Sanger and Illumina

Question 32

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?

Answer 32

220 base pairs

Question 33

What method requires an amplification step prior to sequencing?

Answer 33

Illumina

Question 34

What are promoters?

Answer 34

Specific RNA polymerase binding sites on DNA

Question 35

What is the difference between the RNA polymerase core and the RNA polymerase holoenzyme?

Answer 35

The holoenzyme binds promoters more tightly than the core enzyme because of the sigma factor

Question 36

Which subunit of RNA polymerase binds to the -35 and -10 boxes of prokaryotic promoters?

Answer 36

Sigma

Question 37

When are the genes within the lac operon induced?

Answer 37

In the presence of low concentrations of glucose

Question 38

Which of the following subunits of prokaryotic RNA polymerase bind to UP elements within promoters?

Answer 38

Alpha

Question 39

In lambda phage, what is the function of N?

Answer 39

It is an antiterminator protein that binds to its own transcript

Question 40

In the forensic use of DNA for identification of individuals using PCR and VNTR minisatellite DNA, PCR primers must be complementary to:

Answer 40

Unique DNA sequences not included in the variable number tandem repeats

Question 41

What mechanism do transposons move by?

Answer 41

Cut and paste

Question 42

What mechanism do retrotransposons move by?

Answer 42

Copy and paste

Question 43

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?

Answer 43

1550

Question 44

Genes that are transcribed but not translated into protein are classified as:

Answer 44

RNA-coding genes

Question 45

Experiments in which isolated nuclei are treated with micrococcal nuclease provide evidence for:

Answer 45

The existence of nucleosomes

Question 46

In vertebrate animals and plants, the nucleosome core is made up of:

Answer 46

8 histones and 146 bp of DNA

Question 47

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?

Answer 47

``` GFP = screenable NPTII = selectable ```

Question 48

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?

Answer 48

1 x 10^4 bp

Question 49

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?

Answer 49

E.coli

Question 50

What is the function of RAP30?

Answer 50

Mediates binding of TFIIF to the core

Question 51

Which part of helix-turn-helix domains bind in the major groove, and which part binds in the minor groove on the opposite side?

Answer 51

Major: recognition helix Minor: N-terminus

Question 52

What is the most common DNA binding motif?

Answer 52

2 hydrogen bonds formed between Arginine side chain of the transcription factor and the guanine base of DNA

Question 53

How do hormone receptors bind DNA?

Answer 53

As a dimer on one face of the DNA double helix, with each subunit in successive major grooves

Question 54

Which groove of the DNA do TBP's bind?

Answer 54

The minor groove; forcing open the DNA

Question 55

What are 2 of the main functions of Rpb4/7?

Answer 55

Locks clamp in closed formation and provides a binding surface for RNA exiting the elongating polymerase

Question 56

GTPase Ras

Answer 56

Dominant-negative; bind GDP and stay in inactive state

Question 57

What is the function of the CTD?

Answer 57

Binds proteins involved in capping, splicing, and polyadenylating precursor mRNAs

Question 58

Genes O & P

Answer 58

Code for the proteins needed for phage DNA replication

Question 59

How does PRE help to promote lysogeny?

Answer 59

It direct transcription leftward through cro & cl, producing antisense product of cro (since cro is usually transcribed rightward from PR)

Question 60

Where is PRE located?

Answer 60

To the right of PR and cro

Question 61

What is the consensus bind sequence of bHLH proteins?

Answer 61

5'-CANNTG-3'

Question 62

When can a lysogen enter lytic phase?

Answer 62

When it encounters mutagenic chemicals, UV light, or radiation

Question 63

What is meant by "processive"?

Answer 63

Antitermination factors remain associated with polymerase as it moves down the DNA