Microbial Genetics EXAMS 1,2,3

How is a nucleoside different from a nucleotide?

• A nucleoside is a sugar, base, and one or more phosphates; a nucleotide does not have phosphates

• A nucleotide is a sugar, base, and one or more phosphates; a nucleoside does not have phosphates

• A nucleoside is a sugar and one or more phosphates; a nucleotide is a sugar, base, and one or more phosphates

• A nucleotide is a sugar and one or more phosphates; a nucleoside is a sugar, base, and one or more phosphates

A nucleotide is a sugar, base, and one or more phosphates; a nucleoside does not have phosphates

What does dNDP stand for?

• Dideoxynucleoside diphosphate

• Deoxynucleoside diphosphate

• Double-stranded nucleotide diphosphate

• Degraded nucleotide diphosphate

Deoxynucleoside diphosphate

How are uracil bases and thymine bases different?

• Uracil has a methyl group that thymine lacks

• Thymine has a 5-methyl group on the pyrimidine ring while uracil does not

• Thymine is a purine and uracil is a pyrimidine

• Uracil contains an extra amino group

Thymine has a 5-methyl group on the pyrimidine ring while uracil does not

When nucleotides are strung together in DNA or RNA which positions on the sugar are connected between the nucleotides?

• 1' carbon to 6' carbon

• 5' OH of one sugar to 3' phosphate of the next

• 3' OH of one sugar to 5' phosphate of the next

• 2' OH of one sugar to 5' phosphate of the next

3' OH of one sugar to 5' phosphate of the next

Which bases are purines?

• Adenine and Guanine

• Cytosine and Thymine

• Uracil and Cytosine

• Adenine and Cytosine

Adenine and Guanine

Which class of bases (purines or pyrimidines) have a two ring structure?

• Purines

• Pyrimidines

• Both

• Neither

Purines

Which base pairs are held together the strongest in double strand DNA?

• Adenine and Thymine

• Guanine and Cytosine

• Adenine and Uracil

• Thymine and Uracil

Guanine and Cytosine

Between what two chemical functional groups are the major hydrogen bond interactions between bases in double strand DNA?

• Amine and phosphate groups

• Amine and oxo groups

• Oxo groups and sugar hydroxyls

• Oxo groups and phosphate

Amine and oxo groups

Ribonucleotide reductase does what reaction?

• Phosphorylates ribonucleotides

• Reduces ribonucleotides (NDPs) to deoxyribonucleotides (dNDPs)

• Converts dNTPs to NTPs

• Removes bases from nucleotides

Reduces ribonucleotides (NDPs) to deoxyribonucleotides (dNDPs)

Thymidylate synthase does what reaction?

• Demethylates dTMP to dUMP

• Methylates dUMP to form dTMP

• Methylates UMP to form TMP

• Methylates an accidental uracil base in double strand DNA to thymine

Methylates dUMP to form dTMP

Why are the two strands of DNA called antiparallel?

A. They both run 5' to 3' in the same direction

B. They are mirror images with the same polarity

C. One strand runs 5' to 3' and the opposite strand runs 3' to 5' (opposite polarity)

D. They are oriented with reversed bases

C. One strand runs 5' to 3' and the opposite strand runs 3' to 5' (opposite polarity)

DNA polymerase catalyzes a nucleophilic attack between which two groups?

A. 3' hydroxyl of the growing strand and the beta phosphate of incoming dNTP

B. 3' hydroxyl of the growing strand and the alpha phosphate of incoming dNTP

C. 3' hydroxyl of the growing strand and the gamma phosphate of incoming dNTP

D. 3' phosphate of the growing strand and the 5' hydroxyl of incoming dNTP

B. 3' hydroxyl of the growing strand and the alpha phosphate of incoming dNTP

Why is the enzyme pyrophosphatase important for DNA replication?

A. It synthesizes pyrophosphate which is added to dNMP to make dNTP

B. It hydrolyzes released pyrophosphate (PPi) to inorganic phosphate making polymerization energetically favorable

C. It removes primers from DNA

D. It ligates Okazaki fragments

B. It hydrolyzes released pyrophosphate (PPi) to inorganic phosphate making polymerization energetically favorable

The template for DNA replication is read in which direction?

A. 5' to 3'

B. 3' to 5'

B. 3' to 5'

What activity does DNA Polymerase I have that DNA Polymerase III does not have?

A. 5' to 3' synthesis activity

B. 5' to 3' exonuclease activity

C. 3' to 5' exonuclease activity

D. 3' to 5' synthesis activity

E. This is a trick question! They both have exactly the same activities!

B. 5' to 3' exonuclease activity

Why does helicase (DnaB) require ATP?

A. To synthesize the primer for replication

B. To provide energy for strand separation (unwinding DNA)

C. To ligate DNA fragments

D. To provide energy to rewind the DNA after replication

E. Two or more of these answers are correct

B. To provide energy for strand separation (unwinding DNA)

Why is the DnaA protein important?

A. It removes primers

B. It initiates chromosome replication

C. It ligates Okazaki fragments together

D. It synthesizes the first primer needed for chromosome replication

E. More than one of these answers is correct

B. It initiates chromosome replication

What does Primase (DnaG) do?

A. Synthesizes short DNA primers at the replication fork

B. Synthesizes short RNA primers at the replication fork

C. Synthesizes primers only at oriC

D. Works with DnaA protein to prime the replication reaction by recruiting helicase to the replication fork

B. Synthesizes short RNA primers at the replication fork

In order to connect two DNAs using ligase what two chemical groups must be present?

A. 5' OH and 3' phosphate

B. 3' OH and 5' phosphate

C. 3' phosphate and 5' phosphate

D. 3' hydroxyl and 5' hydroxyl

B. 3' OH and 5' phosphate

What two enzymes make up the primosome?

A. DNA polymerase I and DNA polymerase III

B. Helicase (DnaB) and primase (DnaG)

C. DnaA and Primase (DnaG)

D. DNA polymerase I and Primase (DnaG)

B. Helicase (DnaB) and primase (DnaG)

What very important job does the clamp loader protein do?

A. Loads helicase to the oriC region to start separating the DNA strands

B. Loads primase (DnaG) at multiple places during replication

C. Helps load DNA polymerase III to the correct place in the replication fork

D. Helps load DNA polymerase I to the correct place in the replication fork

E. Helps load both DNA polymerase I and III to the correct place in the replication fork

C. Helps load DNA polymerase III to the correct place in the replication fork

What is the difference between the leading and the lagging strand in DNA replication?

A. The leading strand is synthesized in the 5' to 3' direction while the lagging strand is synthesized in the 3' to 5' direction

B. The leading strand is synthesized continuously while the lagging strand is synthesized discontinuously

C. Leading strand synthesis is primarily by DNA polymerase III while lagging strand synthesis is primarily by DNA polymerase I

D. The lagging strand is synthesized continuously while the leading strand is synthesized discontinuously

E. More than one of these answers are correct

B. The leading strand is synthesized continuously while the lagging strand is synthesized discontinuously

Why is an AT rich DNA region important next to the OriC?

A. The DnaA protein binds to AT rich regions

B. The double strand helix separates more easily in AT rich regions

C. Helicase binds to AT rich regions

D. Primase binds to AT rich regions

E. More than one of these answers is correct

B. The double strand helix separates more easily in AT rich regions

Why does DnaA require ATP to initiate chromosome replication?

A. ATP is used to synthesize primers

B. ATP is a measure of energy in the cell

C. ATP is used to methylate the OriC sequence

D. ATP is used to phosphorylate the OriC sequence (kinase reaction)

B. ATP is a measure of energy in the cell

To initiate DNA replication what does DnaA do at OriC?

A. DnaA synthesizes the first primer for replication

B. DnaA binds and supertwists the OriC region

C. DnaA interacts directly with the primosome

D. DnaA nicks the OriC region to make a 3' hydroxyl in the DNA to prime replication

B. DnaA binds and supertwists the OriC region

When replication begins at E. coli OriC how many replication forks are made?

A. Only one replication fork

B. Two replication forks moving in opposite directions

C. Two replication forks moving in the same direction

D. Zero replication forks

B. Two replication forks moving in opposite directions

Why are TerA and TerB spaced apart and not right next to each other?

A. It is easier to stop replication by not having the replication forks pass each other

B. To allow the two replication forks to pass each other to create an overlapping sequence

C. Because sometimes TerA doesn't stop replication so TerB is a backup point for termination

D. To allow the chromosome to replicate twice before terminating replication

B. To allow the two replication forks to pass each other to create an overlapping sequence

What enzyme does the Tus protein stop?

A. Primase

B. Helicase

C. DNA Polymerase III

D. DnaA

E. Clamp loader

B. Helicase

Which is not true of Topoisomerase IV?

A. All answers are true

B. Separates the two daughter DNA molecules at the end of chromosome replication

C. Cuts both strands of one daughter DNA molecule

D. Requires ATP

A. All answers are true

Type I topoisomerases do what?

A. Release energy from the DNA when twisting by +1

B. Add energy to the DNA when twisting by +1

C. Add energy to the DNA when twisting by +2

D. Release energy from the DNA when twisting by -2

A. Release energy from the DNA when twisting by +1

What is a plaque?

A. A "hole" in a film (lawn) of E. coli on an agar plate where the bacteria have been lysed by an added phage

B. The film (lawn) of E. coli on an agar plate where the bacteria have not been lysed by an added phage

C. The film (lawn) of E. coli on an agar plate (without any phage added)

D. A phage that lyses bacteria

A. A "hole" in a film (lawn) of E. coli on an agar plate where the bacteria have been lysed by an added phage

Which of the following statements is not true for Type I II III and IV restriction-modification enzymes?

A. None of the restriction enzymes can cut modified DNA

B. Some enzymes cut (nick) one strand of the DNA and some enzymes cut both strands of the DNA

C. Type II enzymes are the restriction enzymes most commonly used in cloning experiments

D. Are involved in recognizing "self" and destroying phage DNA coming in from outside of the cell

A. None of the restriction enzymes can cut modified DNA

Why is it important that Type I II and III restriction enzymes come in pairs of restriction and modification activities?

A. The restriction enzyme repairs DNA and modification cuts it

B. Modification protects host DNA from cleavage by its own restriction enzyme

C. Invading DNA needs to be modified before a restriction enzyme can cut it

D. After restriction the cut site is modified to prevent ligase from reconnecting the cut ends

B. Modification protects host DNA from cleavage by its own restriction enzyme

When separating DNA on an agarose gel it is important to remember that?

A. DNA moves to the positive pole of the electric current

B. DNA moves to the negative pole of the electric current

C. Cut DNA moves to the positive pole but negatively supercoiled DNA moves to the negative pole

D. Cut DNA moves to the negative pole but negatively supercoiled DNA moves to the positive pole

A. DNA moves to the positive pole of the electric current

Why is DNA ligase important for DNA cloning experiments?

A. It connects DNA fragments during a PCR reaction

B. It joins DNA fragments by sealing nicks in the sticky ends region

C. It adds an ATP to the DNA making it one base pair longer

D. It adds a dATP to the DNA making it one base pair longer

B. It joins DNA fragments by sealing nicks in the sticky ends region

DNA hybridization experiments are based on what principle?

A. A single strand DNA probe can find a complementary single strand DNA sequence match in a solution

B. A single strand DNA probe can find a complementary double strand DNA sequence match in a solution

C. A double strand DNA probe can find a complementary double strand DNA sequence match in a solution

D. A double strand DNA probe can find a complementary single strand DNA sequence match in a solution

A. A single strand DNA probe can find a complementary single strand DNA sequence match in a solution

The process of nick translation to label DNA involves what?

A. DNaseI and DNA polymerase I

B. DNaseI and either DNA polymerase I or Klenow fragment of DNA polymerase I

C. DNaseI and Klenow fragment of DNA polymerase I

D. Only Klenow fragment of DNA polymerase I

A. DNaseI and DNA polymerase I

Can Klenow fragment do both nick translation and strand displacement DNA synthesis?

A. Yes

B. No it can only do strand displacement synthesis

C. No it can only do nick translation synthesis

D. No it can't do either nick translation or strand displacement synthesis

B. No it can only do strand displacement synthesis

How does fluorescent detection in Southern and Northern hybridization experiments depend on antibodies?

A. The antibody sticks to the probe DNA

B. The antibody sticks to double strand molecules and not single strand molecules

C. The antibody sticks to the target DNA

D. The probe is synthesized with an antibody attached which then binds a fluorescent molecule

A. The antibody sticks to the probe DNA

When using a DNA polymerase to label DNA with radioactive sulfur it is important to do what?

A. Use a dNTP that has a radioactive sulfur in place of the alpha phosphate

B. Use a dNTP that has a radioactive sulfur in place of the gamma phosphate

C. Use a dNTP that has a radioactive sulfur in place of the 3' hydroxyl

D. Use a dNTP that has a radioactive sulfur in place of the 5' hydroxyl

E. Use a dNTP that has a radioactive sulfur in place of one of the nitrogens in the base ring

A. Use a dNTP that has a radioactive sulfur in place of the alpha phosphate

A thermostable DNA polymerase is used in PCR because?

A. PCR requires cycles of high and low temperatures

B. PCR is carried out at a constant high temperature

C. PCR takes hours so the enzyme needs to be highly stable

D. Thermostable DNA polymerases are better at unwinding DNA during replication

A. PCR requires cycles of high and low temperatures

Which statements are correct?

A. A mutant has a mutation

B. A mutation is a mutant

C. Any mutation makes a strain an auxotroph

D. Two of these answers are true

E. Three of these answers are true

A. A mutant has a mutation

If a mutation is called a A136G variant what does that mean?

A. The 136th alanine (A) in the protein has been changed to a glycine (G)

B. The 136th glycine (G) in the protein has been changed to an alanine (A)

C. The 136th adenine (A) in the gene has been changed to a guanine (G)

D. The 136th guanine (G) in the gene has been changed to an adenine (A)

A. The 136th alanine (A) in the protein has been changed to a glycine (G)

A catabolic mutation is what?

A. Is a mutation in a gene coding for a protein involved in utilizing a carbon source

B. Is a mutation in a gene coding for a protein involved in making an essential growth substance

C. Is a mutation that causes the inability to either use a carbon source or make an essential growth substance

D. Results in an auxotroph

E. Two or more of these answers are correct

A. Is a mutation in a gene coding for a protein involved in utilizing a carbon source

Which pairs of independently derived mutations are alleles?

A. hisA2 and hisA4

B. hisA2 and hisB2

C. hisA2 and hisB4

D. hisA2 and proA2

A. hisA2 and hisA4

If the guanine in dGTP is oxidized and incorporated into DNA during replication by DNA polymerase opposite an adenine what type of mutation would result?

A. A transversion mutation

B. A transition mutation

C. A null mutation

D. A "Game of Thrones" mutation

A. A transversion mutation

What is an example of tautomerization of a DNA base?

A. An oxo group changing to an amine group

B. An oxo group changing to a hydroxyl group

C. A DNA base being methylated

D. More than one of these answers is correct

B. An oxo group changing to a hydroxyl group

At high temperatures cytosine deaminates and forms which base?

A. Thymine

B. Uracil

C. Adenine

D. Guanine

B. Uracil

What is a missense mutation?

A. A mutation that creates a stop codon

B. A mutation that changes one amino acid to another

C. A mutation that adds an extra base to the DNA

D. A mutation that removes a base from the DNA

B. A mutation that changes one amino acid to another

If the two sequences 5'-AAAGGG-3' and 5'-CCCTTT-3' flank a 2000 base pair region of DNA what would happen if recombination occurs at those sequences?

A. The DNA region would invert (make an inversion mutation)

B. The DNA region would delete (make a deletion mutation)

C. The DNA region would duplicate

D. Nothing recombination cannot occur at those two sequence

A. The DNA region would invert (make an inversion mutation)

Which of the following is correct about lesions and mutations?

A. A lesion can become a mutation

B. A lesion is a mutation

C. A lesion can become a mutant

D. A mutation can become a lesion

A. A lesion can become a mutation

Why is replication needed to make a mutation from an oxidized guanine base (GO) in the DNA molecule?

A. Replication will sometimes add an adenine opposite the GO base in the DNA

B. Replication will sometimes add a cytosine opposite the GO base in the DNA

C. Replication will sometimes add a thymine opposite the GO base in the DNA

D. None of these answers are correct replication is not needed to make a mutation when GO is in the DNA

A. Replication will sometimes add an adenine opposite the GO base in the DNA

If methylcytosine is deaminated what base does it form?

A. Thymine

B. Uracil

C. Adenine

D. Guanine

A. Thymine

If a base is deaminated what functional group replaces the amine group?

A. A carbonyl group (oxygen attached to a carbon by a double bond)

B. A methyl group

C. An amino group

D. A hydroxyl group (oxygen attached to a carbon by a single bond)

A. A carbonyl group (oxygen attached to a carbon by a double bond)

What does an N-glycosylase do?

A. Removes a damaged base by cleaving the bond between the sugar and the base

B. Removes a damaged base by cleaving the bond between the phosphate and the base

C. Nicks the DNA backbone next to a damaged base

D. Reduces the deoxyribose sugar attached to a damaged base to a ribose sugar

A. Removes a damaged base by cleaving the bond between the sugar and the base

What is an AP site in DNA?

A. A sugar without a base attached

B. A pyrimidine dimer

C. A purine dimer

D. A gap in the DNA backbone where a sugar is missing

E. More than one of these answers is correct

A. A sugar without a base attached

What does an AP nuclease do?

A. Nicks the DNA backbone at an AP site

B. Adds a base to a sugar at an AP site in the DNA

C. Cleaves the covalent bonds connecting two bases in a pyrimidine dimer

D. Acts as a 5' to 3' exonuclease to remove a section of one strand of the DNA

A. Nicks the DNA backbone at an AP site

What is the correct order of enzymes involved in removal and repair of uracil in DNA?

A. Uracil N-glycosylase AP nuclease DNA polymerase and ligase

B. AP nuclease uracil N-glycosylase DNA polymerase and ligase

C. Uracil N-glycosylase AP nuclease helicase DNA polymerase and ligase

D. Uracil N-glycosylase AP nuclease helicase exonuclease DNA polymerase and ligase

A. Uracil N-glycosylase AP nuclease DNA polymerase and ligase

What is the correct order of enzymes in the removal and repair of GO in DNA by MutM?

A. MutM AP lyase AP nuclease DNA polymerase and ligase

B. AP nuclease MutM AP lyase DNA polymerase and ligase

C. MutM AP lyase helicase DNA polymerase and ligase

D. MutM AP lyase exonuclease DNA polymerase and ligase

D. MutM AP lyase exonuclease DNA polymerase and ligase

What type of mutation does very short patch repair correct?

A. A methylcytosine deaminating to a thymine

B. A cytosine deaminating to a thymine

C. A cytosine deaminating to a uracil

D. A methylcytosine deaminating to a uracil

E. Two of these answers are correct

A. A methylcytosine deaminating to a thymine

What reaction does the very short patch repair enzyme perform?

A. Nicks the DNA backbone next to the incorrect base

B. Removes the incorrect base from the deoxyribose sugar

C. Nicks the opposite strand of the backbone from the incorrect base

D. Removes a small region of one DNA strand by nicking the backbone twice about 10 bases apart

A. Nicks the DNA backbone next to the incorrect base

What reaction does MutY N-glycosidase do to repair oxygen damage to a guanine (GO base)?

A. Removes the adenine opposite the GO from the deoxyribose sugar in the backbone

B. Removes the GO from the deoxyribose sugar in the backbone

C. Removes the cytosine opposite the GO from the deoxyribose sugar in the backbone

D. Removes the deoxyribose sugar attached to the GO from the DNA backbone

A. Removes the adenine opposite the GO from the deoxyribose sugar in the backbone

For repair of an alkylated base in the DNA which of the following is NOT a mechanism for repair of this base damage?

A. An N-glycosidase to remove the damaged base

B. A methyltransferase to remove the alkyl group from the base

C. A dioxygenase to oxidize the methyl group

D. A reductase to reduce the methyl group

D. A reductase to reduce the methyl group

In order to get more bacterial mutations with UV light what should you do?

A. After exposure to intense UV light wrap the petri dish in aluminum foil and put it in a dark incubator

B. After exposure to intense UV light incubate the petri dish in a glass incubator near a window

C. After exposure to intense UV light incubate the petri dish at room temperature near a window

D. Two of these answers are correct

A. After exposure to intense UV light wrap the petri dish in aluminum foil and put it in a dark incubator

The enzyme photolyase is the most efficient way to repair damage caused by UV light. When will this enzyme NOT work?

A. In the dark

B. In bright light

C. When the cell is low on energy (ATP)

D. When the cell is being photographed

A. In the dark

Thymine dimers can be repaired by a specific N-glycosylase initiated pathway. What is true of this repair pathway?

A. One of the two thymines in the dimer are cleaved from the DNA backbone and the DNA backbone is nicked on the 5' side of dimer

B. One of the two thymines in the dimer are cleaved from the DNA backbone and the DNA backbone is nicked on the 3' side of dimer

C. Both of the two thymines in the dimer are cleaved from the DNA backbone and the DNA backbone is nicked on the 5' side of dimer

D. Both of the two thymines in the dimer are cleaved from the DNA backbone and the DNA backbone is nicked on the 3' side of dimer

A. One of the two thymines in the dimer are cleaved from the DNA backbone and the DNA backbone is nicked on the 5' side of dimer

The nucleotide excision repair pathway is one way to repair a distortion in the DNA. Which of the following is the correct order of steps in this repair pathway?

B. Find the distortion cleave the backbone on the 5' side of the distortion unwind the DNA excise the nucleotide replicate the opposite strand and use ligase to connect

C. Find the distortion cleave the backbone on the 3' side of the distortion unwind the DNA excise the nucleotide replicate the opposite strand and use ligase to connect

D. Find the distortion cleave the backbone on the opposite strand from the distortion unwind the DNA excise the nucleotide replicate the DNA and use ligase to connect

A. Find the distortion cleave the backbone on both sides of the distortion unwind the DNA excise the nucleotide replicate the opposite strand and use ligase to connect

The methyl-directed mismatch repair pathway is one way to repair a distortion in the DNA. Which of the following is the correct order of steps in this repair pathway?

A. Find the distortion cleave the backbone on both sides of the distortion unwind the DNA excise the nucleotide replicate the opposite strand and use ligase to connect

B. Find the distortion cleave the backbone on the 5' side of the distortion unwind the DNA excise the nucleotide replicate the opposite strand and use ligase to connect

C. Find the distortion cleave the backbone on the 3' side of the distortion unwind the DNA excise the nucleotide replicate the opposite strand and use ligase to connect

D. Find the distortion cleave the backbone on the opposite strand from the distortion unwind the DNA excise the nucleotide replicate the DNA and use ligase to connect

C. Find the distortion cleave the backbone on the 3' side of the distortion unwind the DNA excise the nucleotide replicate the opposite strand and use ligase to connect

The protein UvrD is involved in both the nucleotide excision repair pathway and the methyl-directed mismatch repair pathway. What activity does UvrD have?

A. Helicase

B. Polymerase

C. Nickase

D. Exonuclease

A. Helicase

Major distortion repair (nucleotide excision repair) and minor distortion repair (methyl directed mismatch repair) have what in common?

A. Both methods remove one strand of the DNA double helix

B. Both methods recognize methylated bases

C. Both methods involve DNA polymerase I

D. Both methods utilize exonuclease enzymes

E. Two or more of these answers are correct

A. Both methods remove one strand of the DNA double helix

Why is it important that the minor distortion repair process occurs immediately after replication?

A. MutH recognizes hemimethylated DNA

B. MutS recognizes newly synthesized DNA

C. MutL links to DNA Polymerase III during replication

D. Dam methylase at the replication fork signals to MutH

A. MutH recognizes hemimethylated DNA

What does MFD stand for?

A. Mutation Frequency Decline

B. mRNA Fixing or Dying

C. Mutants Frequently Die

D. mRNA Fixes DNA

A. Mutation Frequency Decline

The MFD protein in transcription coupled repair recruits what protein to repair DNA damage?

A. UvrA in nucleotide excision repair

B. MutS in methyl-directed mismatch repair

C. Photolyase in pyrimidine dimer repair

D. VSR endonuclease in very short patch repair

A. UvrA in nucleotide excision repair

What is the importance of the inverted repeats at the ends of the transposable element?

A. This is where the transposase enzyme binds and cuts the DNA

B. This is where RecA binds with help from the transposase enzyme

C. This is where SSB binds with help from the transposase enzyme

D. This is where DNA polymerase binds with help from the transposase enzyme

A. This is where the transposase enzyme binds and cuts the DNA

Why are there direct repeats outside of a transposable element?

A. Because the transposase cuts the target in a staggered fashion resulting in a direct repeat

B. Because the transposase cuts the inverted repeats of the transposable element and duplicates them by inversion making direct repeats

C. Because the transposase replicates the inverted repeats of the transposable element making direct repeats

D. Because the transposase flips one inverted repeat of the transposable element during insertion making direct repeats

E. Because the transposase cuts the two identical ends of the transposon which results in a direct repeat sequence when the transposon is inserted into the target

A. Because the transposase cuts the target in a staggered fashion resulting in a direct repeat

For transposition which statement is true?

A. Both simple and replicative transposition require DNA polymerase

B. Only simple transposition requires DNA polymerase

C. Only replicative transposition requires DNA polymerase

D. Neither simple nor replicative transposition requires DNA polymerase

A. Both simple and replicative transposition require DNA polymerase

In a composite transposon which region(s) can not move to a new location?

A. One of the insertion sequences along with the "something else" region

B. The insertion sequence on the "left" side

C. The insertion sequence on the "right" side

D. Both insertion sequences along with the "something else" region

E. All of these regions can move to a new location

A. One of the insertion sequences along with the "something else" region

In Tn5 transposition the ends of the transposable element DNA are protected how?

A. By connecting the 5' and 3' ends of the DNA together to make a hairpin structure

B. By the transposase enzyme holding onto the ends

C. By replicative transposition which connects the transposable element ends directly to the recipient

D. By the action of DNA ligase connecting the two ends of the DNA to make a circle

A. By connecting the 5' and 3' ends of the DNA together to make a hairpin structure

What serves as the primer for replication in Tn3 replicative transposition?

A. The 3' ends of the transposon

B. The 5' ends of the transposon

C. The 3' ends of the recipient DNA

D. The 5' ends of the recipient DNA

E. Both the 3' ends of the transposon and the 3' ends of the recipient DNA

C. The 3' ends of the recipient DNA

A resolvase enzyme is needed for transposition of what?

A. A noncomposite transposable element

B. A composite transposable element

C. An insertion sequence

D. More than one of these answers is correct

A. A noncomposite transposable element

A charged Tn5 transposon or transposome is one that?

A. Has the transposase enzyme attached to both ends

B. Has the transposase enzyme attached to one end

C. Has inserted one end of the transposon into the target DNA

D. Has inserted both ends of the transposon into the target DNA

E. Is the transposon in the new location after transposition has been completed

A. Has the transposase enzyme attached to both ends

Which is not true about transposition?

A. Transposition always involves a resolvase

B. Transposition always involves DNA polymerase I

C. Transposition always involves DNA ligase

D. Transposition always involves a transposase

E. Two or more of these answers are not true

A. Transposition always involves a resolvase

In cut-and-paste transposition what is replicated?

A. The target site DNA

B. The entire transposon

C. The inverted repeats on the two ends

D. There is no replication in cut-and-paste transposition

A. The target site DNA

What is a cointegrate in transposition?

A. A DNA molecule containing both donor and target replicons (circles)

B. The initial complex formed in transposition before replication begins

C. The DNA molecule removed from the donor in cut and paste transposition

D. The DNA molecules formed by a resolvase

A. A DNA molecule containing both donor and target replicons (circles)

Replicative transposition is what type of replication?

A. Semiconservative

B. Conservative

C. Dispersive

D. None of these answers is correct

A. A DNA molecule containing both donor and target replicons (circles)

Which is not a site specific recombinase?

A. Transposase

B. Integrase

C. Resolvase

D. Invertase

E. None of the above (all are site specific recombinases)

A. Transposase

If a site specific recombination enzyme acts on two direct repeats in a single DNA molecule what will happen?

A. The DNA molecule will separate into two separate DNA molecules each with one copy of the direct repeat

B. The DNA molecule will separate into two separate DNA molecules each with two copies of the direct repeat

C. The region between the direct repeats will flip to the opposite orientation with the repeats still in the direct orientation

D. The region between the direct repeats will flip to the opposite orientation but now the repeats will be in the indirect or opposite orientation

A. The DNA molecule will separate into two separate DNA molecules each with one copy of the direct repeat

Invertases function to do what?

A. Flip a promoter between two genes

B. Move a gene to a new place in the genome

C. Make sure antibiotic resistance genes are in the correct orientation in an integron

D. Remove lambda from the chromosome after it has been inserted

A. Flip a promoter between two genes

The Y and S recombinase families function in a similar manner by doing what?

A. Attaching a hydroxyl group on the enzyme to a phosphate in the DNA backbone

B. Attaching a hydroxyl group on the enzyme to a sugar in the DNA backbone

C. Attaching an amino group on the enzyme to a phosphate in the DNA

D. Attaching a carboxyl group on the enzyme to a sugar in the DNA

A. Attaching a hydroxyl group on the enzyme to a phosphate in the DNA backbone

In site specific recombination there are Recombinase Binding Elements (RBE) and Crossover (cleavage) points. Which of the following is true about the relationship between RBEs and Crossover points?

A. A Crossover point is between two RBEs

B. Two Crossover points flank one RBE

C. Two Crossover points are flanked by two RBEs

D. One Crossover point is next to one RBE

A. A Crossover point is between two RBEs

For recombination by a site specific recombination enzyme what other enzymes must be involved in the recombination process?

A. No other enzymes are required

B. RecA

C. Ligase

D. Both DNA polymerase and ligase

E. Helicase

A. No other enzymes are required

In the RecBCD pathway RecA is loaded onto what?

A. The 3' single stranded end region of a DNA molecule

B. The 5' single stranded end region of a DNA molecule

C. Both the 5' and 3' single stranded regions on one end of a DNA molecule

D. The 5' single stranded region on one end of a DNA molecule and the 3' single stranded region at the other end of the same DNA molecule

A. The 3' single stranded end region of a DNA molecule

In RecBCD initiated recombination what is the correct sequence of events?

A. RecBCD directly loads RecA on the single stranded DNA

B. SSB binds the single stranded DNA first and then RecA binds

C. SSB and RecA work together to bind the single stranded DNA

D. RecA binds the DNA first and then SSB binds

E. More than one of these is correct

A. RecBCD directly loads RecA on the single stranded DNA

What is the correct order of RecBCD complex activities in loading RecA to the DNA molecule?

A. 3' to 5' exonuclease endonuclease 5' to 3' exonuclease RecA loading

B. 5' to 3' exonuclease endonuclease 3' to 5' exonuclease RecA loading

C. 5' to 3' exonuclease endonuclease 5' to 3' exonuclease RecA loading

D. Endonuclease 3' to 5' exonuclease 5' to 3' exonuclease RecA loading

E. 5' to 3' exonuclease 3' to 5' exonuclease endonuclease RecA loading

A. 3' to 5' exonuclease endonuclease 5' to 3' exonuclease RecA loading

The RecF complex RecFOR does what activities?

A. Replaces SSB with RecA

B. Unwinds DNA (helicase activity)

C. Removes one strand of the DNA (exonuclease activity)

D. Adds SSB to the single strand gapped DNA

E. Two or more of these are correct

A. Replaces SSB with RecA

RecA-mediated recombination requires sequences that are what?

A. Homologous

B. Humongous

C. AT rich

D. GC rich

A. Homologous

RecA promotes what?

A. Invasion of the 3' end of a RecA coated single strand DNA into a double strand DNA target

B. Invasion of the 5' end of a RecA coated single strand DNA into a double strand DNA target

C. Invasion of a RecA coated double stranded DNA into a double strand DNA target

D. Invasion of a RecA coated double stranded DNA into a RecA coated double strand DNA target

A. Invasion of the 3' end of a RecA coated single strand DNA into a double strand DNA target

Spooling in RecA mediated strand invasion does what?

A. Makes the D loop bigger

B. Makes the D loop smaller

C. Destroys the D loop

D. Makes a D loop

A. Makes the D loop bigger

RecA mediated recombination can result in a swapped DNA region. What enzyme increases the amount of DNA that is exchanged?

A. RuvAB

B. Helicase

C. Either RecFOR or RecBCD

D. RuvC

A. RuvAB

What does cooperative binding of RecA mean?

A. RecA binding promotes additional RecA binding nearby

B. RecA binding is in cooperation with SSB binding

C. RecA binding is in cooperation with RecBCD or RecF

D. RecA binding is in cooperation with RecBCD or RecF and with SS

A. RecA binding promotes additional RecA binding nearby