Exam 4 Practice Questions

Transcriptional control
In gene regulation, which type pf control is the most efficient?
Initiation will be inhibited because sigma cannot bind to the promoter
. How is a mutation in a bacterial cell that deletes three base pairs 10 base pairs upstream from the +1 site likely to affect transcription and why?

A. Initiation will be inhibited because RNA polymerase core enzyme cannot bind to the promoter.
B. Termination will not occur because hairpin secondary structure cannot form.
C. A three-base-pair deletion is too small to have an effect.
D. Initiation will be inhibited because sigma cannot bind to the promoter

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C. a single nucleotide deletion in an exon coding for an active site
Which of the following mutations is most likely to cause a phenotypic change?

A. a nucleotide substitution in an exon coding for a transmembrane domain
B. a frameshift mutation one codon away from the 3′ end of the nontemplate strand
C. a single nucleotide deletion in an exon coding for an active site
D. a duplication of all or most introns
E. a large inversion whose ends are each in the same region between genes

D. Several transcription factors have bound to the promoter
In eukaryotic cells, transcription cannot begin until _____.

A. the 5′ caps are removed from the mRNA
B. the DNA introns are removed from the template
C. the two DNA strands have been cleaved by topoisomerase
D. Several transcription factors have bound to the promoter
E. DNA nucleases have isolated the transcription unit

C. the sigma factor
In E coli If RNA polymerase is missing _____, then transcription initiation would not occur at the appropriate initiation sites.

A. amino acids
B. the core
C. the sigma factor

A. bind the sigma subunit that is associated with RNA polymerase
David Pribnow studied the base sequences of promoters in bacteria and bacterial viruses. He found two conserved regions in these promoters (the -10 box and the -35 box). These two regions of the promoter _____.

A. bind the sigma subunit that is associated with RNA polymerase
B. attach the correct nucleotide triphosphate to the template DNA strand
C. signal the initiation site
D. separate the two DNA strands

A. The molecule is digested by enzymes because it is not protected at the 5′ end.
. In an experimental situation, a student researcher inserts an mRNA molecule into a eukaryotic cell after she has removed its 5′ cap and poly-A tail. Which of the following would you expect her to find?

A. The molecule is digested by enzymes because it is not protected at the 5′ end.
B. The cell adds a new poly-A tail to the mRNA.
C. The mRNA attaches to a ribosome and is translated, but more slowly.
D. The mRNA is quickly converted into a ribosomal subunit

A. a sequence in DNA near the site for transcription, where RNA polymerase bind
A promoter is ______

A. a sequence in DNA near the site for transcription, where RNA polymerase bind
B. one or more eukaryotic proteins that bind to DNA near the start of a gene
C. a sequence in RNA that promotes the release of RNA polymerase from DNA
D. a protein that associates with bacterial RNA polymerase to help it bind to DNA

C. RNA splicing removes introns
Which one of the following statements about RNA processing is true?

A. A primary transcript is often much shorter than the final RNA molecule that leaves the nucleus.
B. Exons are cut out before mRNA leaves the nucleus.
C. RNA splicing removes introns
D. RNA splicing can be catalyzed by tRNA.

E. an RNA with catalytic activity
A ribozyme is _____.

A. a catalyst that uses RNA as a substrate
B. an enzyme that synthesizes RNA as part of the transcription process
C. an enzyme that synthesizes RNA primers during DNA replication
D. an enzyme that catalyzes the association between the large and small ribosomal subunits
E. an RNA with catalytic activity

D. 3, 1, 2, 5, 4
Put the following events of transcription in chronological order. 1 Sigma binds to the promoter region. 2 The double helix of DNA is unwound, breaking hydrogen bonds between complementary strands. 3 Sigma binds to RNA polymerase. 4 Sigma is released. 5 Transcription begins.

A. 3, 2, 1, 4, 5
B. 2, 3, 4, 5, 1
C. 2, 3, 1, 4, 5
D. 3, 1, 2, 5, 4

cannot grow in a particular environment
replica plating is used to isolate mutants that
they are all controlled by the same promoter
Why are the genes involved in lactose metabolism considered to be an operon?
the repressor is not bound to the inducer
in the lac operon, the repressor inhibits transcription when
activators bind to regulatory sequences in ___ and to___ polymerase
when glucose and another sugar is present in the environment, inducer exclusion prevents the use of the other sugar and allows only use of glucose
How does inducer exclusion control gene expression in the lac operon
one type of regulator of transcription
a regulon is a set of genes controlled by
the repressor would always be bound to DNA
Predict what would happen if the lac repressor protein were altered so it could not bind to the inducer
Production of RNA
Production of a protein
How can we tell if a gene is being expressed?
differential cell expression
Cells differ due to
A gene product is actively being synthesized
Used in a cell
When does gene expression occur?
DNA —> mRNA —-> protein —-. activated protein
Flow of information
What is the most energy efficient type of control?
Post-Translational…. why…. USES MORE ENERGY
What is the fastest form of control?
The process of growing bacteria on an agar plate, then transferring a copy of that growth to other plates using a sterile velvet pad. Analysis of growth patterns on the secondary plates gives information about the genetic properties of the growing bacteria.

-screens for mutants!!!!!!!!

Replica Plating
a group of genes that operate together
Lac Z,Y,A
What makes up the lac operon?
shuts down expression of lacZ and lacY
In the absence of lactose the lacI gene product…..
Binds directly to the lacI repressor
Causes it to release from the operator (allosteric control)
Ends negative control of the operon
Lactose is the inducer
In the presence of lactose (when glucose is absent) ……
does not allow the import of lactose.
This phenomenon is called inducer exclusion
When glucose is present…
cAMP sends a signal “HEY WE ARE DYING ,SOS!!”
binds to (CAP), which in turn allows the CAP to bind to upstream of the promoter which assists the RNA Polymerase in binding to the DNA. Transcription is on.
What happens when glucose begins to deplete?
positive and negative control
Transcriptional control can be regulated via
Bacterial gene regulation in which the binding of a regulatory protein (activator) to regulatory DNA sequence stimulates transcription.
positive control
genetic expression occurs unless it is shut off by some form of a regulator molecule
Negative control
ara operon
Example of positive control
an activator
AraC protein is ____ when bound to arabinose
Arac protein is a ___ when arabinose is absent
collection of genes or operons that are transcriptionally co-regulated
The first gene in the lac operon of E. coli that codes for enzyme B-galactosidase.
encodes the lactose permease, required for transport of lactose into the cell
controls lacZ, lacY and lacA; that codes for a repressor protein
acetyl transferase
short DNA region, adjacent to the promoter of a prokaryotic operon, that binds repressor proteins responsible for controlling the rate of transcription of the operon
The inducer (lactose) in the lac operon binds to the repressor which causes a shape change. What type of regulation is this?
The regulation of multiple bacterial genes that are not part of one operon.
Global Gene Regulation
INTERNAL environment
The cells in a multicellular EUKARYOTE express different genes in response to changes in the…
1. Chromatin remodeling
2. Transcipion
3. RNA processing
4.mRNA stability
6. post translational

*side note first 3 steps occur in nucleus and last 3 occur in cytoplasm

Regulation of genes in Euk. in ORDER
Chromatin is arranged into…
-Condensed parts of
-Decondensed (loosened)
parts of chromatin——— ACTIVE
-HAT – histone acetyl transferase (adds acetyl group)
-HDAC – histone deacetylase (removes acetyl group)
– adding methyl=condense
-adding acetyl=decondense
Chromatin Remodeling
pass from one cell generation to the next but do not alter the DNA sequence

-Histone acetylation
Histone methylation
DNA methylation

Epigenetic changes
regulatory sequences on the DNA.
Regulatory transcription factors are proteins that bind
to ….
1.promotor proximal elements
2. enhancers
3. silencers
Types of regulatory sequences
Are located just upstream of the promoter and the transcription start site
-both positive and negative
promoter proximal elements
A DNA sequence that recognizes certain transcription factors that can stimulate transcription of nearby genes.
-can work even if the orientation flipped (5′-3′).
-positive, NOT next to promoter
bind to DNA sequences and inhibit the start of transcription.
-negative control, NOT next to promoter
More than one kind of mature, processed mRNA
Consisting of different combinations of transcribed exons
mRNA Stability
Alternative Splicing
1.RNA interference

2.By phosphorylation of a certain ribosomal protein

Control of Translation
1.Transcription of genes that code for hairpin RNAs

2.Hairpin RNA transported to cytoplasm where the hairpin loop is cut out.

3.One strand is taken up by the RNA -induced splicing complex (RISC) …now called a microRNA

4.MicroRNA binds to target mRNA

5.RISC cuts the mRNA and prevents translation!!

limits life span

RNA Interference (microRNA)
Folding and assembling into the tertiary and quaternary structures by chaperone proteins.

2. Transportation to the final destination

3. Modifications by adding various groups (eg: phosphates, sugars, lipids)

4. Degradation of the protein – get a ubiquitin tag and a proteasome destroys it.

Post Translational
the complex of DNA and proteins found in eukaryotic nuclei
What is chromatin?
They are found in a variety of locations and are functional in any orientation
What is true about enhancers?
The set of reg. transcription factors
In eukaryotes, what allows only certain genes to be expressed in certain types of cells?
reg. transcription factors such as activators
What types of proteins bind to the promoter- proximal elements?
RNA template
Reverse transcriptase catalyzes the synthesis of DNa from an….
Complementary DNA. DNA produced synthetically by reverse transcribing mRNA. Because of eukaryotic mRNA splicing, cDNA contains no introns.
producing many copies of a gene
DNA cloning
A small, circular section of extra DNA that confers one or more traits to a bacterium and can be reproduced separately from the main bacterial genetic code.
make copies of foreign DNA
A bacterial enzyme that recognizes a specific DNA nucleotide sequence and that cuts the double helix at a specific site within the sequence.

only cut at palindromes

Restriction endonuclease
Cells that take up DNA from the environment and incorporate into their genomes
A random collection of DNA fragments from an organism cloned into a vector
DNA library
A limited gene library using complementary DNA. The library includes only the genes that were transcribed in the cells examined.
cDNA library
Single stranded fragment that will bind to a particular sequence in a mixture of DNAs. By binding to the target sequence, the probe marks the fragment containing that sequence distinguishing from the other fragments
A method of producing thousands of copies of DNA segment using the enzyme DNA polymerase
Polymerase chain reaction
(1) heat the DNA strands to about 94 degrees C to separate the strands
(2) add the primers to the separated strands and allow the primers to combine (or hybridize) with the strands by lowering the temperature to about 60 degrees C
(3) add the DNA polymerase and a mixture of free nucleotides (G,A,T,C) to the separated strands. Heat the test tube to 72 degrees C and the polymerase enzyme directs the rebuilding of a double stranded DNA molecule; the process is repeated 25 to 30 times
Steps of PCR
DNA is made in the lab, but some of the bases are altered, and cause the growing DNA chain to end at that base. These altered bases are dideoxy nucleotides
Dideoxy sequencing
Variations in DNA sequence that occur when a single nucleotide in the genome is changed
single nucleotide polymorphisms
lacks OH- group
When present in a DNA synthesis reaction mixture, a ddNTP molecule is added to the growing chain of DNA. No further nucleotides can be added afterward. Why?
D. the small subunit of the ribosome recognizes and attaches to the 5′ cap of mRNA
Which of the following is the first event to take place in translation in eukaryotes? elongation of the polypeptide
A. covalent bonding between the first two amino acids
B. base pairing of activated methionine-tRNA to AUG of the messenger RNA
C. binding of the larger ribosomal subunit to smaller ribosomal subunits
D. the small subunit of the ribosome recognizes and attaches to the 5′ cap of mRNA
C. mRNA, tRNA, and rRNA
Translation requires _____
A. mRNA, DNA, and rRNA
B. mRNA, tRNA, and DNA
C. mRNA, tRNA, and rRNA
D. mRNA, tRNA, DNA, and rRNA
B. A site
. During elongation, which site in the ribosome represents the location where a codon is being read?
A. P site
B. A site
C. E site
D. the small ribosomal subunit
What does a bacterial RNA polymerase produce when it transcribes a protein-coding gene?
C. pre-mRNA
B. A stop codon is reached.
How does termination of translation take place?
A. The poly-A tail is reached.
B. A stop codon is reached.
C. The end of the mRNA molecule is reached.
D. The 5′ cap is reached.
A. high and glucose levels are low
The greatest expression of the lac operon occurs when lactose levels are _____ .
A. high and glucose levels are low
B. low and glucose levels are high
C. high and glucose levels are high
D. low and glucose levels are low
A. a
At which of the following stages does transcriptional control occur?
DNA —(a) —> mRNA —(b) —> protein —(c) —> activated protein

A. a
B. b
C. c
D. All of the answers represent transcription.
E. None of the answers represents transcription

A. always produce β-galactosidase
An E. coli cell without a functional lacI gene is expected to _____.
A. always produce β-galactosidase
B. be unable to metabolize lactose within the cell
C. be unable to transport lactose into the cell
D. never produce β-galactosidase
C) III, II, IV, V, I
What is the most logical sequence of steps for splicing foreign DNA into a plasmid and inserting the plasmid into a bacterium.

I. Transform bacteria with a recombinant DNA molecule.
II. Cut the plasmid DNA using restriction enzymes.
III. Extract plasmid DNA from bacterial cells.
IV. Hydrogen-bond the plasmid DNA to nonplasmid DNA fragments.
V. Use ligase to seal plasmid DNA to nonplasmid DNA.

DNA copies of retroviral genomes become integrated into the genome of the infected cell.
For application in gene therapy, what is the most favorable characteristic of retroviruses?
genes that code for reg. proteins
Although the expression of most genes is tightly regulated, some genes are expressed at roughly constant rates. Which of the following genes would you predict to be constitutively (constantly) expressed?
the lac operon would be transcribed continually
According to the lac operon model proposed by Jacob and Monrod, what is predicted to occur if the operator is removed from the operon ?
Put the following events of elongation in prokaryotic translation in chronological order. 1. binding of mRNA with small ribosomal subuint 2. recognition of initiation codon 3. complementary base pairing between initiation codon and anticodon of initiatior tRNA 4. base pairing of the mRNA codon following the initiator codon with its complementary tRNA
Select one:
a. 1,2,3,4,5
b. 2,1,4,3,5
c. 1,2,3,5,4
d. 5,4,3,2,1
All possible nucleotide sequences that could encode a portion of a polypeptide can be synthesized and used as probes
How can amino acid sequence be used to design a gene specific hybridization probe?
mRNA, tRNA, ribosomes, GTP
Translation directly involves
reverse transcriptase
What is needed to make cDNA from RNA?
parking break
The product of the lacI genes functions as the cars
If a scientist needs to put a new DNA into bacterium she must___ the bacterium
reverse transcriptase to reconstruct the gene from its mRNA
A gene that contains introns can be made shorter for genetic engineering purposes by
it induces transcription by binding to the repressor and causing its release from the operator
What is the role pf lactose in regulating lac operon expression>
different DNA fragments ligated into different plasmids
A gene library from a particular human’s retinal cell would be a collection of?
Introns are noncoding segments of DNA that are present in the initial transcript, but are removed by splicing
As scientists were unraveling the mysteries associated with transcription and translation in euk.s they discovered there was not a one-to-one correspondence between the nucleotide sequence of the gene and the base sequence of the mRNA it codes for. They proposed the genes-in-pieces hypothesis. How can this hypothesis be explained?
the choice of primers
What controls which DNA is amplified in PCR?
How many copies of DNa do we get after 4 cycles of PCR?
B. To separate the DNA strands
What is the purpose of heating DNA in PCR?
A. To kill any contaminating bacteria.
B. To separate the DNA strands.
C. To denature any contaminating enzymes in the sample.
D. To activate the deoxyribonucleotides
C. dNTPs
PCR utilizes specific DNA primers and a thermo stable polymerase enzyme to amplify (make many copies of) a particular DNA sequence (typically 100-600 bases long). Double stranded DNA (dsDNA) must first be separated and primers anneal (complimentary base pair to) their targeted sequences. Polymerase can then extend the DNA strands. What must also be added to the mixture besides primers and polymerase enzymes in order to have amplification of DNA?

B. RNA polymerase
C. dNTPs
D. electron carriers
E. DNA repair enzymes

One round of heating and cooling in PCR = 1 cycle and doubles the amount of DNA. After 3 cycles, how much DNA would you expect if your starting sample had 3pg of target DNA?
Acts as a cofactor for polymerase
Magnesium chloride (MgCl2) is also required for amplification of target DNA by PCR. Which of the following is likely a role of Mg+ in this technique?

A. Acts as a cofactor for polymerase
B. Acts as an allosteric inhibitor of polymerase
C. Makes the solution hypertonic to the polymerase enzyme
D. The positive charge of the Mg+ ions neutralize the negative charges of the phosphate groups of nucleotides for a more efficient reaction
E. Allows for easy isolation of the newly synthesized DNA by charge sorting.

C. DNA is often the starting material for PCR so the viral genome is first reverse transcribed into DNA
Another application of the Polymerase Chain Reaction (PCR) is to screen samples for the presence of viruses. For example, remember the recent Ebola outbreak? In the US, if a patient is suspected of having clinical symptoms and is at high risk for exposure to Ebola virus, one technique to determine if that person is infected with Ebola is to send a blood sample for PCR based analysis. In this assay, many copies of specific DNA sequences are made in order to cross a detection threshold.
Each Ebola virus is composed of single strand of RNA approximately 18,950 nucleotides long enclosed within a cylindrical viral envelope. In some laboratories, the first step might be to incubate samples with the enzyme Reverse Transcriptase. Why might this be?

A. The polymerase chain reaction is identical to all transcription reactions.
B. DNA is often the starting material for PCR so the viral genome is first transcribed into RNA.
C. DNA is often the starting material for PCR so the viral genome is first reverse transcribed into DNA.
D. In PCR, RNA primers bind to specific regions of DNA not RNA so the RNA must first be converted to DNA.

D. be cut by the same restriction enzyme
In order to insert a human gene into a plasmid, both must _____

A. have identical DNA sequences
B. originate from the same type of cell
C. code for the same gene product
D. be cut by the same restriction enzyme
E. be the same length

E. transformation
What name is given to the process where plasmid is introduced in E. coli?

A. transduction
B. translation
C. conjugation
D. cloning
E. transformation

D. cloning
The gene on plasmid is replicating in bacteria, which term describe it the best

A. transduction
B. translation
C. conjugation
D. cloning
E. transformation

A. different DNA fragments ligated into different plasmids
A gene library from a particular human’s retinal cell would be a collection of _____.

A. different DNA fragments ligated into different plasmids
B. DNAs cut by a restriction enzyme
C. Plasmids cut by a restriction enzyme
D. PCR-amplified DNAs
E. genes that have been sequenced from a particular organism

E. reverse transcriptase
If mRNAs could be ligated and replicated within plasmids, what enzyme commonly used in recombinant DNA technology would no longer be needed?

A. RNA polymerase
B. Taq polymerase
C. restriction enzymes
D. DNA polymerase
E. reverse transcriptase

A. a plasmid used to transfer DNA into a living cell
In recombinant DNA methods, the term vector can refer to _____.

A. a plasmid used to transfer DNA into a living cell
B. the “sticky end” of a DNA fragment
C. a DNA probe used to identify a particular gene
D. a SNP marker
E. the enzyme (endonuclease) that cuts DNA into restriction fragments

D. It could be used to create a complete genomic library
Which of the following would NOT be true of cDNA produced using human brain tissue as the starting material?

A. It could be amplified by the polymerase chain reaction.
B. It lacks the introns of the human genes.
C. It could be used as a probe to detect genes expressed in the brain.
D. It could be used to create a complete genomic library.
E. It was produced from mRNA using reverse transcriptase.

C. It lacks a 3′ OH.
When present in a DNA synthesis reaction mixture, a ddNTP molecule is added to the growing chain of DNA. No further nucleotides can be added afterward. Why?

A. It lacks a 5′ phosphate group.
B. It irreversibly binds to the active site of DNA polymerase.
C. It lacks a 3′ OH.
D. It prevents the association of DNA polymerase and DNA chain.

B. size or length
The DNAs produced in a DNA sequencing reaction are analyzed on the basis of their ______.

A. length of time needed for cloning
B. size or length
C. positive charge
D. shape

B. sequence a DNA fragment
A laboratory might use dideoxyribonucleotides to _____.

A. clone the breakpoints of cut DNA
B. sequence a DNA fragment
C. produce cDNA from mRNA
D. separate DNA fragments
E. visualize DNA expression


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