UF AGR3303 exam 2

The kind of gene whose product interacts with other nucleotide sequences to affect their transcription or translation is a:

a. constitutive gene.

b. regulatory gene.

c. structural gene.

d. protein-coding gene.

b. regulatory gene

Regulation of gene activity can occur at several points in the pathway of information flow. Which of the following types of regulation takes place primarily in eukaryotes?

a. modification of chromatin

b. transcriptional regulation

c. translational regulation

d. posttranslational modification

e. regulation of mRNA processing and stability

a. modification of chromatin

A typical operon in prokaryotic cell contains several regions. In which region does a regulator protein bind?

a. structural genes

b. terminator

c. operator

d. none of the above

c. operator

For a(n) __________ operon, transcription normally takes place, and it is turned off by a(n) _________.

a. inducible; active activator

b. inducible; active repressor

c. repressible; active activator

d. repressible; active repressor

d. repressible; active repressor

Low levels of glucose lead to all of the following, EXCEPT that:

a. cAMP levels increase.

b. permease levels increase.

c. b-galactosidase levels increase.

d. lac operon is activated.

e. CAP-cAMP loses its affinity to DNA.

e. CAP-cAMP loses its affinity to DNA.

The trp operon repressor has two binding sites. What two things bind the repressor?

a. tryptophan, DNA

b. first DNA site, second DNA site

c. first tryptophan molecule, second tryptophan molecule

a. tryptophan, DNA

When tryptophan concentrations are high in an E coli cell, what happens?

a. Tryptophan binds the repressor

b. Repressor becomes active.

c. The tryptophan synthesis genes are not transcribed.

d. All of the above.

d. All of the above.

E.coli lac operon control by lac I

a. negative inducible

b. negative repressible

c. positive inducible

d. positive repressible

a. negative inducible

E. coli lac operon control by CAP

a. negative inducible

b. negative repressible

c. positive inducible

d. positive repressible

d. positive repressible

An operon is controlled by a repressor. When the repressor binds to a small molecule, it binds to DNA on the operon, which prevents the operon expression.

a. negative inducible

b. negative repressible

c. positive inducible

d. positive repressible

b. negative repressible

An operon is controlled by a repressor. When the repressor binds to a small molecule, it is released from binding to DNA on the operon and the operon starts to express.

a. negative inducible

b. negative repressible

c. positive inducible

d. positive repressible

a. negative inducible

What is the function of cAMP in regulation of the lac operon?

a. it activates a repressor protein

b. it activates an activator protein

c. it inactivates a repressor protein

d. it inactivates an activator protein

b. it activates an activator protein

Consider regulation by both the lac repressor and CAP (catabolite activator protein), under what environment does the E.coli show a high level of transcription of the lac operon.

a. high glucose, no lactose

b. no glucose, high lactose

c. high glucose, high lactose

d. no glucose, no lactose

b. no glucose, high lactose

Which statement is TRUE about the lac operon regulation?

A. At high glucose and no lactose conditioin, the cAMP level is high and CAP binds the CAP binding site

B. At no glucose and high lactose condition, lac repressor does not bind to the operator and the transcription level is high

C. At high glucose and high lactose condition, allolactose level and cAMP level are very high

D. At no glucose and no lactose level, lac repressor binds to the operator and cAMP level is high

A and C

B and D

B and D

Suppose that a mutant form of GAL80 protein lacks the domain that binds to GAL4 protein. Yeast cells with this mutant GAL80 will:

a. never activate the genes needed for galactose metabolism.

b. always repress the genes needed for galactose metabolism even in the presence of galactose.

c. always activate the genes needed for galactose metabolism even in the absence of galactose.

d. have the minimal (basal) level of transcription of genes for galactose metabolism.

c. always activate the genes needed for galactose metabolism even in the absence of galactose.

In eukaryotes, there are a variety of post-transcriptional mechanisms of gene regulation. Which of these mechanisms acts in the nucleus?

a. alternative splicing of pre-mRNA

b. increased initiation of translation

c. miRNA mediated translational repression

d. addition of phosphate or sugar groups to proteins

a. alternative splicing of pre-mRNA

siRNA and miRNA inhibit gene expression by all of the following EXCEPT:

a. cleaving mRNA.

b. altering chromatin DNA structure.

c. stimulating RNA degradation.

d. stabilizing translation machinery.

d. stabilizing translation machinery.

Which of the following mechanisms of gene regulation is unique to eukaryotic cells?

a. binding of activator proteins to DNA

b. binding of repressor proteins to DNA

c. chromatin remodeling

d. cascades of transcriptional activation

c. chromatin remodeling

A_________, which binds to a core promoter, consists of general transcription factors and RNA polymerase.

a. basal transcription apparatus

b. transcriptional activator

c. regulatory protein

d. RITS

a. basal transcription apparatus

siRNAs __________ the rate of the target mRNA degradation and ___________ the rate of protein production.

a. increase, decrease

b. increase, increase

c. decrease, decrease

d. decrease, increase

a. increase, decrease

Which of the following is true regarding the Arabidopsis FLD gene?

a. FLD deacetylates histones that bind to regions of FLC gene and stimulates its transcription.

b. FLD deacetylates histones surrounding FLD gene, causing suppression of FLD transcription

c. FLD deacetylates histones that bind to FLC gene, causing repression of FLC transcription.

d. FLD causes repression of FLC translation.

c. FLD deacetylates histones that bind to FLC gene, causing repression of FLC transcription.

Choose the type of control illustrated by GAL4 in the control of genes for yeast galactose-metabolizing enzymes.

a. negative inducible

b. negative repressible

c. positive inducible

d. positive repressible

c. positive inducible

Which of these controls of gene activities can take place in eukaryotes.

a. packaging of DNA into chromatin (chromatin structure) and modifications to DNA

b. regulation of transcription

c. processing of RNA transcripts

d. regulation of RNA stability

e. regulation of translation

f. All of the above.

f. All of the above.

Which statement is NOT true.

a. prokaryotes don't have histones and do not package DNA in the same way that eukaryotes do

b. Prokaryotes do not splice introns or add a 5′ cap or poly(A) tail to their mRNA.

c. transcripts in prokaryotes are generally longer-lived than in eukaryotes

c. transcripts in prokaryotes are generally longer-lived than in eukaryotes

Which of the following types of gene mutation in a protein-coding gene usually have the least severe (i.e., deleterious) phenotype?

a. base deletions

b. nonsense substitutions

c. missense substitutions

d. expansion of a trinucleotide repeat

e. All of the above generate equally severe phenotypes.

c. missense substitutions

All of the following are causes of transition mutations EXCEPT:

a. deamination of C to U.

b. wobble base-pairing of T with G.

c. incorporation of 5-BU into DNA and subsequent mispairing of 5-BU with G.

d. oxidation of G and its subsequent mispairing with A.

e. alkylation of G and its subsequent mispairing with T.

d. oxidation of G and its subsequent mispairing with A.

Base analogs are mutagenic because of which characteristic?

a. They produce changes in DNA polymerase that cause it to malfunction

b. They distort the structure of DNA

c. They are similar in structure to the normal bases

d. They chemically modify the normal bases

c. They are similar in structure to the normal bases

Insertion or removal of one or more nucleotide base pairs in DNA usually results in a ____________ mutation.

a. transition

b. frameshift

c. reversion

d. transversion

e. suppressor

b. frameshift

The diagram above demonstrates the steps required for the incorporated G* to induce a stably inherited mutation induced by EMS. What type of mutation above does the EMS induce?

a. transition

b. transversion

c. deamination

d. frameshift

e. mismatch

a. transition

Which is true of transposable elements?

a. They can promote DNA rearrangements.

b. They often generate short flanking direct repeats.

c. Many possess short terminal inverted repeats.

d. They are found in the genomes of all living organisms.

e. All of the above are true.

e. All of the above are true.

Which of the following is NOT true regarding the mutagenic nature of transposition?

a. Insertion of a transposable element can disrupt the function of a gene.

b. Homologous recombination between two transposable elements can cause chromosome inversions.

c. Transposable elements insert into DNA sequences at random and can be useful to researchers for inducing mutations throughout a genome.

d. Mobilization of transposable elements occurs in an unlimited, unregulated manner.

d. Mobilization of transposable elements occurs in an unlimited, unregulated manner.

Which of the following best describes the Activator (Ac) and Dissociation (Ds) transposable elements in maize (corn)?

a. Ac elements cannot transpose unless a Ds element is present.

b. Ac contains a functional transposase gene; Ds lacks a functional transposase gene.

c. Ds contains a functional transposase gene; Ac lacks a functional transposase gene.

d. Both Ac and Ds have functional transposase genes.

e. Neither Ac nor Ds contain functional transposase genes.

b. Ac contains a functional transposase gene; Ds lacks a functional transposase gene.

Most cancers are assumed to arise through which of the following?

a. Errors in transcription

b. The production of unbalanced gametes because of nondisjunction during meiosis.

c. Genetic or epigenetic changes in somatic cells

d. Delayed cell division during early embryogenesis

e. None of the above answers is correct.

c. Genetic or epigenetic changes in somatic cells

Which of the following is the major event associated with the retinoblastoma cancer?

a. A translocation involving chromosomes 9 and 22

b. Both copies of a tumor-suppressor gene are inactivated

c. A translocation results in the enhanced expression of an oncogene

d. A mutation results in an activated RAS oncogene

e. Inactivation of a major DNA repair system

b. Both copies of a tumor-suppressor gene are inactivated

The process by which genetic changes occur in tumors and allows them to become increasingly aggressive over time is called?

a. Clonal evolution

b. Metastasis

c. Loss of heterozygosity

d. Epigenetic evolution

e. Signal transduction

a. Clonal evolution

Which of the following is a process whereby cancer cells travel to other sites in the body and establish secondary tumors?

a. Oncogenesis

b. Angiogenesis

c. Malignancy

d. Secondary

e. tumorigenesis

f. Metastasis

f. Metastasis

Mutations in proto-oncogenes are generally _________ whereas mutations in tumor-suppressor alleles are generally ______________.

a. Deletions; duplications

b. Recessive; dominant

c. Duplications; deletions

d. Dominant; recessive

e. Deletions; base-pair substitutions

d. Dominant; recessive

Which of the following groups of proteins is NOT commonly known to include oncogenes?

a. Transcription factors

b. Growth factors

c. Signal-transduction proteins

d. Ion channels

e. Growth factor receptors

d. Ion channels

Normal cellular genes whose products are involved in facilitating cell division to occur under appropriate conditions are called?

a. Proto-oncogenes

b. Tumor-suppressor genes

c. Passenger genes

d. Inhibitor genesDriver genes

a. Proto-oncogenes

The normal activity of the retinoblastoma (Rb) protein in the cell is to:

a. Inhibit p53 activity

b. Suppress transcription of tumor suppressor genes

c. Regulate the progression of from G1 to S in the cell cycle

d. Induce cyclin-CDK complex formation

e. Block the initiation of anaphase during the cell cycle

c. Regulate the progression of from G1 to S in the cell cycle

Which of the following chromosomal abnormalities is associated with chronic myelogenous leukemia?

a. A deletion

b. An inversion

c. A duplication

d. A reciprocal translocation

e. An aneuploidy involving one of the shorter autosomal chromosomes

d. A reciprocal translocation

In Burkitt lymphoma, there is increased expression of the MYC gene. Which of the following best explains this situation?

a. A chromosome deletion has removed a tumor suppressor gene.

b. A chromosome deletion has removed an oncogene.

c. A chromosome duplication that involves a segment with an oncogene.

d. A translocation has brought the MYC gene next to a different regulatory region.

e. The MYC gene has been amplified.

d. A translocation has brought the MYC gene next to a different regulatory region.

Regulatory genes are genes whose products control the transcription or translation of other genes

true

In bacterial operon, promoter is bound by regulator protein to regulate its transcription

False

The operator is where the regulatory protein binds. The promoter is where RNA pol binds.

A repressible gene should be under control by a repressor

False.

It can be negative repressible (control of repressor) or positive repressible (control of activator)

For a gene under negative control, the regulator protein is a repressor.

True

For a gene under positive inducible control, regulator protein is an activator and normally the gene is inactive in transcription.

True

In the absence of lactose, the lac operon is constitutively transcribed.

False.

Constitutively means always on (like housekeeping), but without lactose, this operon will be off.

Lac operon has both negative and positive controls

True

In the absence of tryptophan, the genes of the trp operon for tryptophan synthesis are not expressed.

False.

They would be on because there is no tryptophan present. The operon is ON to MAKE more tryptophan which is currently lacking. A surplus of tryptophan will actually inhibit (co-repressor) this operon.

In a general sense, highly condensed DNA bound with histone proteins represses gene expression

True

The rate of degradation of mRNAs is important in gene regulation in eukaryotes

true

Addition of Acetyl groups to the tails of histone proteins usually results in repression of transcription.

False

In eukaryotes, most structural genes are found within operons

False

Prokaryotes

FLD deacetylates histones that bind to regions of FLC gene and stimulates its transcription.

False

represses transcription

GAL4 is a transcription repressor for the galactose-digesting enzyme gene

False

activator not repressor

Alternative splicing is known to be important in the regulation of the sexual development in Drosophila

True

RNA interference is also known as RNA silencing and posttranscriptional gene silencing

True

When siRNAs are present, the rate of target mRNA degradation decreases and the rate of protein production increases

False

degradation increases, protein production decreases

During RNA interference, miRNA in RISCs match the mRNA imperfectly and stimulate the translation of targeted mRNA

False

inhibits not stimulates

During RNA interference for cleavage of mRNA, siRNA in RICS pairs with mRNA and RISC cleaves the mRNA

True

RITS consists of miRNAs and proteins

False

It is siRNAs + proteins that forms the RNA induced transcriptional silencing complex.

siRNA in RITS binds to DNA and cause methylation and restricting transcription

True

Somatic mutations are not transmitted to new daughter cells

False

A mutation that changes a G/C base pair to A/T is a transversion mutation

False

translation mutation

Nonsense mutations do not alter the amino acid sequence chain

False

A missense mutation changes a codon that specifies an amino acid into one that terminates translation

False

nonsense

Insertion or removal of one or more nucleotide base pairs in DNA within a gene often results in a frame shift mutation.

True

DNA replication errors are spontaneous mutations

True

Transposition can cause gene mutation

True

UV light can be absorbed by pyrimidine in DNA resulting in pyrimidine dimers

True

During DNA replication, incorporation of 5-Bromouracil can lead to transition mutation

True

Base analogs are mutagenic because they distort the structure of DNA

False

Restriction Enzyme A has the recognition sequence 5′CTGCAG3′. Restriction Enzyme B has the recognition sequence 5′GCGC3′. Based on this information, you can infer that:

a. Enzyme A will cut a genome into more pieces than will Enzyme B.

b. Enzyme A will cut the genome into fewer pieces than will Enzyme B.

c. Enzyme A will generate DNA pieces with blunt ends and Enzyme B will generate DNA pieces with sticky ends.

d. Enzyme A will generate DNA pieces with sticky ends and Enzyme B will generate DNA pieces with blunt ends.

e. none of the above.

b. Enzyme A will cut the genome into fewer pieces than will Enzyme B.

Which of the following is NOT true regarding DNA gel electrophoresis?

a. The agarose gel acts as a molecular sieve separating DNA fragments based on size.

b. Larger DNA fragments will migrate faster than will smaller DNA fragments.

c. By passing an electrical current through the gel, DNA fragments move toward the positive end.

d. Fragments of known size are used to measure the size of the sample DNA.

e. DNA needs to be stained in order to be visualized.

b. Larger DNA fragments will migrate faster than will smaller DNA fragments.

Which is NOT required for PCR?

a. DNA polymerase

b. all four nucleotides

c. target DNA

d. DNA ligase

e. Primers

d. DNA ligase

Gene cloning requires placing the gene of interest into a cloning vector. A good cloning vector must have which of the following?

a. origin of replication

b. selectable markers

c. unique restriction site(s)

d. all of the above

e. only a and c

d. all of the above

A woman claims that her former boyfriend, Mr. X, is the father of her child. X maintains that the child's father is Mr. Y and not him. DNA fingerprints of all four persons are shown below. What can be concluded about the child's paternity?

a. Mr. X is the father.

b. Mr. Y is the father.

c. Neither Mr. X nor Mr. Y is the father.

d. The woman is not this child's mother.

e. Both c and d.

c. Neither Mr. X nor Mr. Y is the father.

Match numbers with the best letter choice:

1. Cloning vector

2. B-galactosidase

3. Ti plasmid

4. PCR

5. Transgene

a. Taq polymerase

b. Agrobacterium tumefaciens

c. Foreign DNA

d. Plasmid

e. lacZ

cloning vector - plasmid

B-gal - lacZ

Ti Plasmid - agrobacterium tumefaciens

PCR - taq polymerase

transgene - foreign DNA

Which is NOT the basic component required for a bacterial cloning vector:

a. unique restriction enzyme cloning site(s)

b. a bacterial origin of replication

c. a selectable marker (e.g., an antibiotic)

d. a promoter for gene expression

d. a promoter for gene expression

Which is NOT true of plasmids?

a. They usually carry essential genes for bacterial survival.

b. Their replication is independent of the chromosomal DNA.

c. They are used extensively in genetic engineering.

d. They contain an origin of replication.

e. They consist of double-stranded DNA.

a. They usually carry essential genes for bacterial survival.

You have discovered a gene that enables organisms to accumulate gold in their tissues by concentrating trace amounts found in normal soil. You want to transfer this gene into a plant. Order the steps below that would accomplish this.

1. Infect the plant with the Agrobacterium strain.

2. Digest the gold gene and a Ti plasmid with appropriate restriction enzymes.

3. Insert the gold gene into the Ti plasmid.

4. Amplify the gold gene with PCR.

5. Transfer the recombinant Ti plasmid into Agrobacterium tumefaciens.

6. Use a selectable marker to identify plant cells that have integrated the recombinant plasmid into their genome.

a. 4 2 3 5 1 6

b. 4 5 2 3 1 6

c. 4 2 5 1 6 3

d. 4 3 2 5 1 6

a. 4 2 3 5 1 6

When present in small amount in sequencing reactions, dideoxyribonucleotide triphosphates (ddNTPs) terminate the sequencing reaction at different positions in the growing DNA strands. ddNTPs stop a sequencing reaction because they:

a. lack a 5′ phosphate group.

b. have a hydroxyl group at their 5′ end.

c. lack a hydroxyl (-OH) group at their 3′ end.

d. permanently bind to the active site of DNA polymerase.

e. cause DNA polymerase to fall off the template strand.

c. lack a hydroxyl (-OH) group at their 3′ end.

What is the function of dideoxynucleotides in Sanger DNA sequencing?

a. They act as primers for DNA polymerase.

b. They act as primers for reverse transcriptase.

c. They cut the sequenced DNA at specific sites.

d. They allow only the specific sequencing of the RNAs of a genome.

e. They stop synthesis at a specific site, so the base at that site can be determined

e. They stop synthesis at a specific site, so the base at that site can be determined

Compared to the original Sanger method of DNA sequencing, 2nd generation sequencing method:

a. have made sequencing faster.

b. allow millions to billions of DNA fragments to be simultaneously sequenced.

c. produce much longer reads in one reaction.

both a and b.

both b and c.

both a and b.

Which of the following statement is NOT true for Illumina sequencing?

a. Cluster reaction in cBot machine generates millions of clonally amplified sequencing template on each cluster

b. Billions of DNA fragments are simultaneously sequenced

c. a light signal is generated when a nucleotide with reversible terminator is cooperated during DNA synthesis to read the sequence.

d. it is a standard procedure and has been used for more than 40 years.

d. it is a standard procedure and has been used for more than 40 years.

During the Illumina sequencing reaction, ______________A solution containing each four deoxynucleotide triphosphate (dNTP) flows over the flow cell one by one.

a. When a nucleotide is added to the growing chain, PPi is released and produces a light-emitting chemical reaction.

b. An X-ray film is used to capture the radioactive signal

c. a solution containing each four deoxynucleotide triphosphate (dNTP) flows over the flow cell one by one

d. When a nucleotide with reversible terminator is incorporated into the growing chain and a florescent signal is produced.

d. When a nucleotide with reversible terminator is incorporated into the growing chain and a florescent signal is produced.

Which of the following statement is NOT true for the 2nd generation sequencing technologies?

a. The throughput of Sanger sequencing is similar to the 2nd generation sequencing methods

b. Illumina sequencing is a 2nd generation sequencing technology

c. clonal amplification is a necessary step

d. for the sample preparation, adapters are added to the end of DNA fragments, which will be used for the sequencing reaction

a. The throughput of Sanger sequencing is similar to the 2nd generation sequencing methods

The clonal amplification for DNA fragments is necessary for 2nd generation sequencing because:

a. 2nd generation sequencing needs to sequence large number of DNA.

b. Sequencing signal of clonal fragments can be strong enough to be detected by the optical detector

c. it can generate more reads data for the analysis

d. it increase the efficiency of DNA polymerase during sequencing by synthesis

e. None of above options

b. Sequencing signal of clonal fragments can be strong enough to be detected by the optical detector

PCR has three recurring steps: denaturation, primer annealing, and hybridization

False

the third step is prier extension

Taq polymerase enzyme, used for PCR, denatures at 94C

False

dsDNA not taq polymerase enzyme

Aragose-gel electrophoresis can be used separate DNA or RNA molecules only on the basis of their electrical charge

False

based on size and electrical charge

Restriction enzymes randomly cut dsDNA and produce either cohesive or blunt ends

False

they do not cut randomly

Plasmid is a small circular DNA of thousands of bp with functional genes but does not have its own origin of replication

False

they do have their own origin of replication

A cloning vector has three important characteristics: 1. Origin of replication. 2. selectable marker 3. unique restriction enzymes

True

During gene cloning, the vector DNA sequence with foreign DNA will integrate into the host genomic DNA. When the host cell divides, copies of the recombinant DNA molecules are passed to the progeny

False

does not integrate into the host

After gene cloning, bacteria with 'empty' or no insert plasmids are blue because they have a functional lacZ. So we are not selecting the blue colony for the cloned gene

True

An expression vector is needed for GMO

True

Ti plasmid can be modified or engineered as a vector for plant transformation

True

The tumor inducing genes in Ti plasmid can be removed and replaced by your gene of interest for plant transformation

True