MICROBIO EXAM 2

What level of regulation is characterized by LacI, TrpR and AraC?
DNA and RNA
Translation
Protein stability
Transcription
Post-transcriptional

Transcription

Which of the following is FALSE about plasmids?
Can be found in eukaryotic microorganisms
Contain essential genes
Require an oriP region for replication
Are circular and sunercoled
Can replicate using a rolling circle mechanism

Contain essential genes

The 50S subunit of the prokaryotic ribosome contains what?
S proteins and 165 rRNA
S proteins, tRNA, and 235 rRNA
L proteins, 235 rRNA and 55 rRNA
S proteins and 235 rRNA
L proteins and 235 rRNA

L proteins and 235 rRNA

During the process of transcription initiation, formation of the closed promoter complex requires what?
Binding of RNAP to a co-repressor
Dissociation of the sigma subunit
Binding of RNAP to the -35/-10 boxes
Binding to the AUG initiation site
Formation of a poly A pause site

Binding of RNAP to the -35/-10 boxes

What is the significance of the AUG codon?
It is a translational pause site
It binds IF1
It codes for nothing (nonsense codon)
It is the initiation (start) codon
It binds release factors

It is the initiation (start) codon

RNA polymerases of archaea are genetically and structurally more similar to bacteria than eukaryotes.
True
False

False

Which of the following is TRUE of Lacl?
It needs to bind ligand to repress transcription
Its ligand is lactose
Its ligand is allolactose
It is a dual regulator of the lac operon
It is the first gene of a 3 gene operon

Its ligand is allolactose

In conjugation, donor DNA is moved into a recipient through what?
A symporter
The transformasome
A mating pilus
A pore complex
The type IV secretion system

A pore complex

Which of the following facts best explains why DNA needs to be replicated in both a continuous and discontinuous manner?
Both strands require an RNA primer
Antiparallelism of DNA strands
Circularized chromosomes
Semiconservative replication
Location of the oriC

Antiparallelism of DNA strands

How many tRNA binding sites can be found in the 70S ribosome of bacteria?
Three
Six
one
Four
None

Three

Which of the following is FALSE about DNA primase (DnaG) in bacteria?
It can ligate Okazaki fragments on the lagging strand
It is an RNA polymerase
It is required for DNA polymerization on both leading and lagging strands
It makes DNA-RNA hetero-duplexes
It is a component of the replisome

It can ligate Okazaki fragments on the lagging strand

Which functional region of tRNA is charged with amino acids?
The D-loop
The T-loop
The anticodon loop
The acceptor end
The tRNA synthase active site

The acceptor end

Which two species of RNA form a duplex at the anticodon loop?
rRNA:mRNA
rRNA:tRNA
tRNA:rRNA
tRNA:mRNA
SRNA:mRNA

tRNA:mRNA

Which of the following is FALSE about IF3 during prokaryotic translation?
It undocks the 30S subunit during termination
It loads the 305 subunit onto RNA during initiation
It binds to the 30S ribosomal unit
Binds to the A site during termination
It is an initiation factor

Binds to the A site during termination

The binding of Tus to hairpin loops leads to the termination of DNA replication in bacteria.
True
False

False

Which of the following is FALSE about termination of DNA replication?
It occurs at ter clusters ter sites are composed of DNA
It may require the help of termination proteins, such as Tus
Both replication forks have their own termination fork traps
ter sites can be found anywhere on the chromosome

ter sites can be found anywhere on the chromosome

RNA polymerase can only initiate transcription with the help of a sigma factor.
True
False

True

Which of the following is FALSE about TrpR?
TrpR binds the end product of the tryptophan biosynthetic pathway
In the absence of its ligand, TrpR is an aporepressor
When repressing the trp operon, TrpR binds to an operator
TrpR can also activate the trp operon when tryptophan levels are low
Tryptophan is the co-repressor of TrpR

TrpR can also activate the trp operon when tryptophan levels are low

In Gram negative species, DNA transformation requires the crossing of two membranes.
True
False

True

Transduction requires which of the following?
A specialized pilus
Entry of phage into bacterial cells
Packing of donor bacterial DNA into phage heads
Rolling circle replication
DNA degradation

Packing of donor bacterial DNA into phage heads

Which of the following is TRUE of prokaryotic sigma factors?
They interact with operators
They guide RNA polymerase to promoters to initiate transcription
They are not required for transcription
They bind to the initiation codon of an mRNA
They are part of the replisome complex

They guide RNA polymerase to promoters to initiate transcription

Which of the following regulates gene expression in prokaryotes at the post-translational level?
Phosphorylation
Promoter
RTP
oriP
AUG

Phosphorylation

Which of the following is TRUE of Rho-dependent termination?
Requires a hairpin-loop at the 3-prime end of the gene
Requires Ter or RTP
Requires ter sites
Requires a rut site
Requires termination factors 1 or 2

Requires a rut site

Which of the following is NOT a building block of DNA?
Purines
Ribose
A triphosphate residue
Pyrimidines
A nitrogenous base

Ribose

What conformation of AraC is needed for repression of the araBAD operon?
AraC with arabinose and bound to both activation sites
AraC with arabinose and bound to one operator and one activator site
AraC without arabinose and bound to one operator and one activator site
AraC bound to both activation sites and RNA polymerase
AraC with arabinose and bound to both operators

AraC without arabinose and bound to one operator and one activator site

In the absence of tryptophan, which of the following is FALSE?
TrpR is an aporepressor
The trp operon is being transcribed
Tryptophan is being synthesized
TrpR is not bound to its ligand
The trp operon is repressed

The trp operon is repressed

**How do you get three proteins out of the bacterial operon pictured below?
*PICTURE*
Three transcriptional units
Three TIRs
Hairpin loops between genes
Exons
Post-transcriptional regulation

Three TIRs

Where do counterclockwise replication forks terminate?
At the oriC site
At clockwise ter sites
At RTP
At counterclockwise ter sites
At Tus

At counterclockwise ter sites

Which of the following is TRUE of topoisomerase I?
It cuts both strands of dsDNA
It hydrolvzes ATP
It introduces supercoils
It relaxes supercoils
It opens the 13-mer replication bubble

It relaxes supercoils

Why are rut sites in non-coding RNA?
So Rho does not collide with RNA polymerase
To allow HP loops to form at pause sites
So Rho does not collide with ribosome
To bind Rho near the RNA polymerase
To allow for the formation of the open promoter complex

So Rho does not collide with ribosome

Which of the following is FALSE about the genetic code?
It contains one start and one stop codon
The code is redundant
It was discovered by the combined efforts of Marshall Nirenberg and Heinrich Matthaei
The code is mostly universal
It consists of nucleotide triplets, termed codons

It contains one start and one stop codon

The F-factor of E. coli encodes genes for which process?
Fertility
Colonization
Transformation
Motilitv
Conjugation

Conjugation

The role for EF-Tu in translation is what?
Peptide bond formation
Dissociation of the 30S and 505 subunits
Termination of translation
Recruitment of charged tRNAs to the A site
Translocation of the 505 ribosome

Recruitment of charged tRNAs to the A site

A single gene can be regulated at multiple levels.
True
False

True

Which of the following is an example of constitutive expression?
The lac operon
Regulated genes
Two-component signal transduction
Unregulated genes
Translation

Unregulated genes

Which of the following is responsible for replacing RNA primers with DNA during DNA synthesis in bacteria?
DnaG, RNA primase
3-prime to 5-prime exonuclease activity of pol Ill
DNA ligase
Pol V
Pol I

Pol I

If the lacA gene were removed (by mutagenesis) from the lacZYA operon, how would this impact transcription initiation from the Placzva promoter?
There would be no transcription initiation
This would have no effect on transcription initiation
There would be no B-galactosidase produced
There would be no translation of operon genes
There would be an increase in transcription initation

This would have no effect on transcription initiation

How does the ribosome know where to initiate translation of mRNA in prokaryotes?
fMet
+1 site
rut sites
TIR
Initiation factor 1

TIR

The spacer is a region of DNA between the -10 box and +1 site in the promoter of a gene
True
False

False

Rank order the following levels of regulation according to regulation response rate from slowest to fastest.
Transcription; translation; post-translational
Transcription; post-translational; translation
Post-translational; translational; transcription
Translation; post-translational; transcription
Translation; transcription; post-translational

Post-translational; translational; transcription

Which of the following is TRUE about the bacterial transformasome?
It is used in the process of conjugation
It requires a specialized pilus structure
Used for rolling-circle replication of plasmids
It moves DNA through a pilus structure
It is used for replicating from the oriP

It requires a specialized pilus structure

The replication bubble in prokaryotic chromosomes forms at the oriC-where does the transcription bubble form during transcription?
Hairpin loop
-35/-10 boxes
ORE
DnaA boxes
UP elements

-35/-10 boxes

Genome size can vary by millions of bases among different strains of the same bacterial species
True
False

True

The p0157 plasmid of E. coli is an example of what?
Broad plasmid host range
Serologic shift
High copy plasmids
Low copy plasmids
Narrow plasmid host range

Narrow plasmid host range

What is one role of nucleoid structuring proteins?
To initiate translation
To restrain/stabilize loop domains of DNA
Folding RNAs into tertiary structures
DNA translocation during conjugation
Supercoiling DNA

To restrain/stabilize loop domains of DNA

What is the purpose of release factor 1?
Initiates replication by binding 9-mer sites at the oriC
Binds to rut sites for Rho-dependent termination
Binds to a stop codon in the A site of a ribosome
Binds to ter sites at replication fork traps
Releases the RNAP from Rho-independent terminators

Binds to a stop codon in the A site of a ribosome

Some prokaryotes have linear chromosomes.
True
False

True

Which is TRUE of aminoacylated tRNAs?
They are uncharged tRNAs in the E site of a ribosome
They are charged with an amino acid
They guide EF-G to the AUG codon
They have a codon
They are translated into protein

They are charged with an amino acid

For highly transcribed genes, re-initiation of transcription can occur repeatedly in bacteria.
True
False

True

It is predicted that Tus binds to what during the termination of DNA replication?

tur

What is the size of an Okazaki fragment in bacteria?

1 kb

What is one role of major grooves in DNA?

Protein-DNA interactions

Which of the following is false about prokaryotic genomes?
They may contain prophages
They can be diploid
They are contained within a nucleoid
they may be linear
They are packaged by NAPs

They can be diploid

What do you propose would happen to the process of DNA replication, if the AT rich 13-mer region were changed to a GC 13-mer region?

Initiation of replication would not occur

Multiple codons can encode the same amino acid.
true
false

true

*Replication of plasmids is dependent on chromosome replication.
true
false

false

The 30S subunit of the prokaryotic ribosome contains what?
S proteins and 165 rRNA
S proteins, tRNA, and 235 rRNA
L proteins, 235 rRNA and 55 rRNA
S proteins and 235 rRNA
L proteins and 235 rRNA

S proteins and 165 rRNA

During the process of transcription initiation, formation of the closed promoter complex requires what?

Binding of RNAP to the -35/-10 boxes

*The stop codon UAG encodes what?

nothing

*During the process of S. pneumoniae transformation, extracellular DNA is trapped by what?

A pilus

Plasmids can replicate in a bidirectional manner, just like circular chromosomes.
true
false

true

Most genes have both coding (i.e. structural) regions as well as non-coding regulatory regions.
true
false

true

Which of the following is FALSE about the role of pili in genetic transfer?
They can bind/trap DNA during the process of transformation
They are used for transformation and conjugation in bacteria
DNA moves through pili during the process of conjugation
The genes for pili are encoded on transferable plasmids called F factors
Type IV pili are used by Gram negative bacteria during transformation

DNA moves through pili during the process of conjugation

RNA polymerase can initiate transcription in the absence of a sigma factor.
true
false

false

When LacI binds to both lac operators, the promoter is looped-out, blocking RNAP binding
true
false

true

Which of the following is a known role of single-stranded binding proteins?
Stabilize single stranded DNA on lagging strand during replication
Stabilize RNA in hairpin loops
Open up the transcription bubble for transcription initiation
Restrain T and D loops in tRNA
Relax supercoiled DNA at replication forks

Stabilize single stranded DNA on lagging strand during replication

which of the following is true of the bacterial relaxosome?
Encoded on a bacteriophage
Encodes a pilus structure
It is a type IV secretion apparatus used for DNA transfer
It is used to termination rolling circle replication
A complex of proteins that transfer DNA during conjugation

A complex of proteins that transfer DNA during conjugation

*Bacteria condense their DNA into a series of protein-bound domains referred to as what?

the nucleoid

In bacteria, the processes of transcription and translation are uncoupled.
true
false

false

Where do clockwise replication forks terminate?
At the oriC site
At clockwise ter sites
At RTP
At counterclockwise ter sites
At Tus

At clockwise ter sites

Which of the following is TRUE of topoisomerase I?
It cuts both strands of dsDNA
It hydrolyzes ATP
It introduces supercoils
It cuts a single strand of DNA
It opens the 13-mer replication bubble

It cuts a single strand of DNA

*In generalized transduction, phages kill the donor and recipient?
true
false

false

The pO157 plasmid is said to have a broad host range because it can be found in many different species of Escherichia coli.

false

One hypothesis for DNA transformation in bacteria is that it is used for DNA repair.

true

If the lacZ gene were removed (by mutagenesis) from the lacZYA operon, how would this impact transcription initiation from the PlacZYA promoter?

This would have no effect on transcription initiation

*How does the ribosome know where to initiate translation of lacZ mRNA?

Start codon

The spacer is a region of DNA between the -35 and -10 boxes in the promoter of a gene.
true
false

true

*IDK?* Rank order the following levels of regulation according to regulation response rate from slowest to fastest.

Transcription; translation; post-translational

How often is the sliding clamp loaded on a leading DNA strand during replication?
once
never
many times
twice
three

once

DnaA is required for initiation of transcription.
true
false

false

*What is meant by the saying, "What is true of E. coli is true of the elephant?"

You can answer any fundamental question about biology using E. coli

*What is one role of nucleoid structuring proteins?

To restrain uncoiling of relaxed DNA

What is the purpose of release factor 1?

Binds to a stop codon in the A site of a ribosome

Some prokaryotes have linear chromosomes.

true

Which is TRUE of aminoacylated tRNAs?

They are charged with an amino acid

For highly transcribed genes, re-initiation of transcription occurs repeatedly in bacteria.

true

2020 set

Some prokaryotes have linear chromosomes.
A. True
B. False

True

Why is it that the human genome is 1000X the size of the E. coli genome, yet only has 8X the number of genes?
A. Many of the mRNAs in human genes are spliced
B. Much more DNA in the human genome is non-coding
C. Much more DNA in E. coli is noncoding
D. Many of the genes in the human genome are redundant
E. The genes in the human genome are much larger

Much more DNA in the human genome is non-coding

DNA-binding proteins commonly interact with what structural region of DNA?
A. Polyphosphate backbone
B. oriP
C. 5-prime ends
D. Hairpin terminators
E. Major groove

Major groove

Bacteria condense their DNA into a series of protein-bound domains referred to as
what?
A. The nucleus
B. The proteome
C. Histone-like proteins
D. The nucleoid
E. The nucleosome

The nucleoid

If you discovered an antibiotic that targeted topoisomerase activity in bacteria, what
process do you hypothesize the antibiotic would directly interfere with?
A. Translation initiation
B. Translation termination
C. Transcription
D. Promoter recognition
E. Conjugation

Transcription

DNA is supercoiled by \________________ and relaxed by \_____________ during the
process of genome packaging.
A. Topo II: helicase
B. Topo II: topo I
C. Topo I: topo II
D. HNS: helicase
E. GyrAB: nucleoid structuring proteins

Topo II: topo I

Where do counterclockwise replication forks terminate?
A. At the oriC site
B. At clockwise ter sites
C. At RTP
D. At counterclockwise ter sites
E. At Tus

At counterclockwise ter sites

Which of the following would interfere with the process of initiation of DNA replication?
A. Swap the clockwise ter clusters with the counterclockwise ter clusters
B. Change the 13-mer AT rich region in the oriC to a 13-mer GC-rich region
C. Remove by deletion the -35 and -10 sites
D. The mutation and loss Rtp
E. The mutation and loss of initiation factor 1

Change the 13-mer AT rich region in the oriC to a 13-mer GC-rich region

If you discovered a new plasmid in the bacterium E. coli, and later discovered the same
plasmid in a different species of bacteria, you would hypothesize that the host range of
the plasmid is what?
A. High
B. Broad
C. Accessory
D. Narrow
E. Non-essential

Broad

Plasmids generally contain genes that are essential to the survival of bacteria and
archaea.
A. True
B. False

False

Herb Boyer cloned what human gene into his pBR322 plasmid, revolutionizing molecular
biology and medicine?
A. Actin
B. PBR
C. Penicillin
D. Insulin
E. Keratin

Insulin

In bacteria, the RNA polymerase holoenzyme is typically comprised of what?
A. 1σ, 2α, β, β' and a ω subunit
B. 1α, 2β and a ω subunit
C. RNA
D. Pol III
E. 2α, β, β' and a ω subunit

1σ, 2α, β, β' and a ω subunit

21. For the cartoon below, identify the transcriptional unit following transcription.

E