Microbial Genomics Final Exam

Which of these are purine bases in DNA?

Adenine and Guanine

A thermostable DNA polymerase is used in PCR because

PCR required cycles of high and low temperatures

If you worked in a laboratory and purchased CTP you would be buying

a chemical that can be incorporated into RNA

The process of nick translation to label DNA involves

DNaseI and DNA polymerase I

What is the genotype of a mutant bacterial strain?

The actual sequences of the mutant strain’s DNA

What is a nucleoside?

A base and sugar

Why are the DNA fragments on the lagging strand during DNA replication called Okazaki fragments?

They are named after Dr. Okazaki who discovered them

Which enzymes do not need ATP?

All of these enzymes use ATP

Examples of hydrogen bonds normally found between bases in DNA double helix are

Amine hydrogen to oxygen oxo group

When using DNA polymerase to label DNA with radioactive sulfur it is important to

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

The protein UvrD is involved in both major and minor distortion repair. What activity does UvrD have?

Helicase

Thymidylate synthase

adds a methyl group to dUMP to make dTMP

A kinase enzyme

adds a phosphate to something

Helicase

unwinds DNA at a replication fork making positive supercoils.

The primer for DNA synthesis must have

a 3’ hydroxyl

For repair of a damaged base, which is the correct order of the enzymes?

DNA glycosylase, AP nuclease, DNA polymerase I, ligase

DNA polymerase proofreading activity

is 3’ to 5’ exonuclease activity

Type II restriction enzymes

Cut between the phosphate and sugar in the DNA backbone always leaving a 5’ phosphate and a 3’ hydroxyl

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?

transversion mutation

To stop E. coli DNA replication at terA and terB sites the Tus protein

stops helicase

When E. coli is growing slowly chromosome replication

is bidirectional around the circle with two replication forks

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

The antibody sticks to the probe DNA

What enzymes removes the RNA primer at the replication forks?

DNA polymerase I

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

Both methods remove one strand of the DNA double helix

Illumina sequencing uses reversible dye termination. Where is the dye attached to cause termination?

the 3’ hydroxyl of a dNTP

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

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

Nonsense mutation suppression involves

a compensating mutation in a tRNA

What does ligase need to connect two DNA strands?

a 3’ hydroxyl and a 5’ phosphate

Which is a transversion mutation

AT base pair to CG base pair

Type I topoisomerases

Releases energy from DNA when twisting by +1

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

DNA moves to the positive pole of the electric current

Which pairs of independently derived mutations are alleles

hisA2 and hisA4

Which is not true of topoisomerase IV?

All answers are true

At the replication fork

The new DNA on both the leading strand and the lagging strand are synthesized in the 5’ to 3’ direction

If the two sequences 5’-AAAGGG-3’ and 5’-CCCTTT-3’ flank a 2,000 base pair region of DNA what would happen if recombination occurs at those sequences?

The DNA region would invert (make an inversion mutations)

If you have a fragment of DNA cut on both ends with the restriction enzymes EcoRI and you wish to ligate the fragment into a cloning vector also cut with a EcoRI how many places will ligase connect the two DNAs together?

Four

Which is not mechanisms to repair an oxidized guanine (GO) in the cell?

Remove a GO opposite an adenine in the DNA

Why is an AT region important at oriC?

AT base pairs are weak so the DNA double helix is more easily opened in AT rich region.

Orphan methylases function in

DNA repair

Which statement are correct?

A mutant has a mutation

A catabolic mutation

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

DNA hybridization experiments are based on what principles?

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

What is a plaque?

a “hole” in a film(lawn) of E. coli on an agar plate where the bacteria has been lysed by an added phage.

A wild type strain is

normal member of species

For a repair a lesion, an AP lyase cut

the sugar phosphate backbone 3’ to the damaged base

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

MutH recognizes hemimethylated DNA

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

none of the restriction enzymes can cut modified DNA

Uracil is sometimes found in DNA. What enzymes starts the process to remove uracil from DNA?

Uracil N-glycosylase

Random priming labeling of DNA involves

Adding hexamer primers to single stranded DNA

In transcription coupled repair

Mfd protein pushes RNA polymerase off the DNA

IF-2 and EF-Tu perform what similar reactions?

Bring in the charged tRNA with the amino acid attached (tRNA-AA)

Sigma subunit if RNA polymerase is important for

promoter recognition

Why are there direct repeats outside of a transposable elements?

because the transposase cuts the target in a staggered fashion, resulting in a direct repeat.

In attenutation control of E. coli tryptophan operon

If translation of trpL is fast then transcription of the rest of the operon is terminated

In E. coli mRNA is degraded

by both 5’ exoribonucleases and 3’ exoribonucleases

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 crossover point is between two RBEs

What is true of the crossover area after recombination of Y and S recombinases?

The crossover area is a double strand hybrid with one strand from each of the two starting molecules.

Attenuation control

stops transcription shortly after it begins

The first amino acid in translation

is placed in the P site of the 30S subunit.

Invertases function to

to flip a promoter between two genes

When a linear double stranded DNA (coming into the cell from transduction for instance) is recombined into the genome by the RecF-RecA method the result is

one daughter DNA with the original double strand DNA and one daughter DNA with the incoming double strand DNA swapped for the original DNA.

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

RuvAB

In factor independent transcription termination

the step loop structure in the mRNA pulls the mRNA away from the RNA polymerase

Riboswitches

are sequences in mRNA that recognized a chemical molecule and control transcription

In control of the B. subtilis tryptophan operon by attenuation

TRAP protein binding to the mRNA causes the terminator loop to form

How are the matching sequencing found in homologous recombination?

Helical nucleoprotein filament of RecA coated DNA scans double strand DNA for a match.

The RecF complex RecFOR does what activity?

replaces SSB with RecA

If recombination happens between two direct repeats then

a region of the DNA will be removed

The beginning of mRNA has

three 5’ phosphate

Where is the formyl group attached on methionine to make formylmethionine?

the N-terminal nitrogen

RecA-mediated recombination requires sequences that are

Homologous

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

attaching a hydroxyl group on the enzymes to a phosphate in the DNA backbone

RHO protein during factor dependent transcription termination

binds to mRNA first

An open complex in transcription is

When the DNA is unwound during transcription initiation

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

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

In the RecBCD pathway RecA is loaded onto

the 3’ single stranded end region of a DNA molecule

In the Tn5 transposition the ends of the transposable elements DNA are protected

by connecting the 5’ and 3’ ends of the DNA together to make a hairpin structure

in RecBDC initiate recombination

RecBCD loads RecA on the single stranded DNA

A polar mutation is one

that has an effect on downstream genes

RecA promotes

invasion of the 3’ end of a RecA coated single strand DNA into a double strand DNA targets.

The tighter RNA polymerase binds to the promoter

the more often transcription initiation will happen

Which statement is true?

Both simple and replicative transposition require DNA polymerase

The first base (+1) in RNA from RNA polymerase transcription is normally a A or a G because

to make cure the cell has enough energy to complete transcription.

In translation of a mRNA by a ribosome the first amino acid of the protein

is always formylmethionine

The wobble hypothesis states that during translation

the 3’ base in the codon does not need to match the 5’ base in the anticodon perfectly

Polycistronic mRNA (operonic mRNA) transcribed from multiple protein coding genes in a row in the genome

has one ribosome binding site in front of each gene that needs to be translated

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

the 3’ ends of the recipient DNA

In factor dependent transcription termination ribosomes can prevent transcription termination because

ribosomes block rut sites on the mRNA

The primary structure of a protein is

the sequence of amino acids

Y and S recombinases

cut the two DNAs to be recombined in a staggered fashion

Phage lambda integrates into the E. coli chromosome by an integrase that recognizes the attB and attP sites. Once integrated into the chromosome the hybrid attP/B sites are in what orientation?

Direct

Chi sites are directional becasue

the limit the amount of DNA removed by RecBCD in one direction vs the other direction.

The 23S “ribozyme” does what rection?

connects the C-terminal end of the growing polypeptides chain to the N-terminal end of the incoming amino acid

Which of the following is true?

two or more of these answers are true

How many phosphates are between the sugars in mRNA?

one

EF-G is needed for which steps of translation?

elongation and termination of transciption

The resolvase enzyme in transposition

separates the two parts of the cointegrate in replicative transposition

Factor independent transcription termination depends on several adenine residues in the template because

adenine: uracil base pairs are weak and promote RNA polymerase releasing the template

Spooling in RecA mediated strand invasion

makes the D loop bigger

Aminoacyl tRNA synthetases charge tRNA with an amino acid by

joining the C-terminal end of the amino acid to the 3’ end of the tRNA