MIC 205A Exam 2

For which of the following can PCR be used?

- identification of individuals - crime scene investigation - paternity testing - recombinant DNA technology

CRISPR function (in correct order)

1. Cas proteins cut entering viral DNA into short fragments. 2. Viral DNA fragments are inserted into a CRISPR array. 3.The bacterial cell transcribes the CRISPR array. 4. crRNAs are generated by the bacterial cell. 5. crRNA binds a Cas nuclease, forming a complex. 6. Cas nuclease-crRNA complex recognizes and destroys DNA of second virus.

DNA polymerases use their ______ activity to remove a mismatched base pair.

3' -- 5' --> exonuclease

The polymerase used in the polymerase chain reaction comes from a thermophilic bacterium. A thermophile grows best between

45° and 80°C

If a 75 base-pair fragment of DNA has 25 cytosines in it, how many adenines would you expect it to have?

50

How many copies of the DNA segment of interest would there be after 3 cycles of the polymerase chain reaction?

8

An open reading frame or a possible protein-encoding region of prokaryotic DNA is

A region of DNA that begins w/ a start codon (ATG) and ends w/ a stop codon

Which regions of the gene (or segment of DNA) shown here encodes the amino acid sequence of a protein?

A,C,E - They encode only exons while introns are spliced out

Consider how an aerobically respiring bacterial cell uses glycolysis, the TCA cycle, and oxidative phosphorylation to break apart and oxidize glucose. What are the three main benefits these central metabolic pathways yield to the cell?

ATP, reduced electron carriers, and precursor metabolites

Phase variation is a phenomenon used by some bacteria (such as E. coli) to evade host immune mechanisms. In this process, the cells

Alternately turn genes off/on to adjust bacterial behavior

Which of the following can serve as selective markers for identifying recombinant bacterial cells?

Antibiotic resistance AND differences in colony phenotype

Changing your T-shirt for one of a different color is analogous to ______.

Antigenic variation

During the process of transformation in the lab setting, cells are plated on selective media to

make sure that only transformants grow

During the entry of the donor DNA into the recipient cell,

one strand is broken down by nucleases

A recombinant organism is

one that that contains genes from another organism

Bacteriophages adsorb or attach

only to members of the same bacterial species.

The donor DNA

pairs with a homologous region of the recipient DNA.

All of the following are desirable features of a cloning host except

pathogenicity

After host cell DNA is broken down by a viral enzyme,

phage DNA is replicated and phage coat proteins are produced.

A difference between transferring plasmids and DNA fragments between bacterial cells is

plasmids can replicate independently

Transformation is facilitated by

proteins on the cell wall that bind DNA.

Transcription is often controlled by DNA-binding proteins. A(n) ______ is a regulatory protein that blocks transcription, while a(n) ______ is a regulatory protein that facilitates transcription.

repressor; activator

If you find that a particular plasmid has an R factor, the bacteria that has it will be

resistant to certain antibiotics

Primers are used for

showing the polymerase enzyme where to begin building the new DNA chain.

During conjugation, the donor chromosome is transferred as

single-stranded DNA

The F pilus binds to

specific receptors on the cell wall of the recipient

Taq polymerase is specifically used in this process because it is

stable at high temperatures

The F plasmid encodes for

the F pilus

After the transfer of the F plasmid is complete

the F- cell becomes F+

Contamination of the sample is a serious concern when doing PCR because:

the contaminant will be amplified, causing a false-positive result.

These dimers are repaired by

the enzyme DNA photolyase and exposure to light.

After the conjugation of an Hfr cell with an F- cell,

the recipient remains F-.

A ______ is used to automatically expose the polymerase chain reaction to repetitive steps, yielding large amounts of DNA in a short period of time.

thermal cycler

The main advantage for bacteria that have the ability to carry out conjugation and other forms of genetic exchange is that

they become genetically diverse

The polymerase chain reaction uses DNA polymerase but not primase or helicase. Helicase is usually responsible for

unzipping the parent DNA strands.

Plasmid DNA is transferred

in single-stranded form

In order for insertional inactivation of a gene to occur, the restriction site must be

in the middle of the gene

In insertional inactivation, if foreign DNA is inserted into the beta-galactosidase gene, the gene is

inactivated, and the colonies are white

In transduction, bacterial DNA is transferred to a new cell when

it is injected by the virus carrying bacterial DNA

You are setting up an enrichment culture to look for methylotrophic bacteria in a sample of water from Lake Washington in Seattle. Methylotrophs are capable of obtaining their carbon and energy needs from single carbon compounds such as methanol. In your enrichment culture, you provide methanol and a variety of macro- and micro-nutrients to encourage growth. However, which of the following must you leave out if you are to successfully enrich for methylotrophs?

Any other carbon source

You are studying the metabolism of the phototrophic green sulfur bacterium Chlorobaculum tepidum and realize that it is running a reversed TCA cycle! How do you explain this observation?

C. tepidum is using the reversed TCA cycle to fix CO2

Antigenic variation is a phenomenon used by some bacteria (such as Neisseria gonorrhoeae) to evade host immune mechanisms. In this process, the cells

Can change the characteristics of certain surface protein on bacteria, forcing immune response to constantly adapt.

Some enzymes require a cofactor or a coenzyme in order to be active. What is the difference between cofactors and coenzymes?

Cofactors are non-protein components that assist enzymes and are typically trace elements; coenzymes are organic cofactors that loosely carry molecules or electrons

The single-stranded ends of DNA molecules can be joined together by

DNA ligase

Which of the following statements regarding transcription and translation is TRUE?

Eukaryotes must splice out introns following transcriptions, while prokaryotes DO NOT.

RNA interference (RNAi) is a mechanism by which

Eukaryotic cells destroy RNA transcripts in a selective and specific manner ton control gene expression

You leave several tomatoes in your refrigerator when you go on vacation. When you get home, the tomatoes are covered in microbial growth. Select ALL the characteristics you can assign to these microbes.

Fastidious

Streptococcus pneumoniae lacks an electron transport chain. Therefore, S. pneumoniae generates ATP via ______.

Fermentation

Which of the following statements regarding bacterial gene control is FALSE?

Genes for constitutive enzymes can be turned off and on as necessary

Why is the DNA heated to over 90 degrees Celsius to start the process?

Heat denatures the DNA, meaning it separates the two strands.

In a CRISPR-Cas system, how does the function of Cas9 used for gene editing differ from that of a Cas used to study gene function?

In gene editing studies, Cas9 cuts the DNA at a specific sequence; in gene function studies, dCas9 binds to but does not cut a specific sequence.

What is the role of Taq polymerase?

It catalyzes the synthesis of the new DNA chains

Why is a selective marker (such as drug resistance) important in recombinant DNA technology?

It makes it possible to easily identify recombinant cells

DNA in cells can encode for thousands of different proteins. Why do cells require mechanisms to regulate expression of the genes that code for these proteins?

Not all proteins are needed at all times, or in equal amounts. Regulating their expression saves time and energy.

In prokaryotic DNA replication, which of the following is FALSE?

On one parent strand, the polymerase synthesizes DNA in the 5' to 3' direction, while on the other it synthesizes DNA in 3' to 5' direction

If a Gram-positive competent cell takes up DNA containing a penicillin resistance gene, what would be added to a selective medium to isolate the transformants?

Penicillin

Anabaena is a genus of filamentous cyanobacteria commonly found in aquatic environments, where it harvests energy from sunlight and fixes both carbon dioxide and nitrogen. Knowing this, how would you classify Anabaena?

Photoautotroph

Greenlake is a small lake in Seattle, WA that sometimes experiences blooms of cyanobacteria, photosynthetic nitrogen-fixing bacteria that typically grow as filaments. These blooms are especially likely to occur during warm summer weather and result in the production of large quantities of biomass that then dies off and decomposes, leading to unpleasant odors. In addition to the aesthetic problems, some strains make toxins that can be dangerous to ingest, leading to the closing of the lake. Treatment of the water with alum (aluminum sulfate) to remove phosphorus from the water has helped to limit growth of cyanobacteria. How would you classify the cyanobacteria from Greenlake in terms of their carbon and energy sources?

Photoautotroph

Removing the electron transport chain of E. coli would

Prevent oxidative phosphorylation

Examples of advantageous genes that can be transferred by transduction are genes for

Sugar fermentation, toxin production, & drug resistance

Two bacterial genes are transduced simultaneously. What does this suggest about the location of the two genes relative to each other?

The two genes must be close together on the bacterial chromosome

Which of the following is FALSE about transposons?

They are capable of moving independently from one cell to another cell.

Why do plasmids work well as vectors for the insertion of foreign DNA?

They can replicate independently of the chromosome They usually contain an identifiable selection marker They contain an origin of replication

Although the actual procedure is much more involved, the basic metabolism of wine-making involves inoculating grape juice with a special strain of the yeast Saccharomyces cerevisiae. S. cerevisiae will preferentially perform aerobic respiration on sugars in the juice but can also ferment those sugars to yield CO2 and alcohol, an important component of wine. Assume you inoculate a completely full container of juice and then close the lid. What will the yeast do?

They will grow aerobically, consume the O2 dissolved in juice, and then switch to fermenting sugars yield alcohol

Why is the DNA cooled slightly after it is denatured?

To allow the primers to anneal to their complementary sequence on the target DNA

What is the general purpose of the PCR process?

To make many copies of a small target piece of DNA.

In order for a cell to make ribosomes, which of the following must be happening?

Transcription and translation

Following the Exxon Valdez oil spill, beaches in Prince William Sound were treated with nitrogen compounds in order to enhance the bioremediation of the oil. What does this tell you about the ecosystem of these beaches?

When the arrival of large quantities of hydrocarbon, nitrogen was a limiting for microbial growth

Generalized transduction occurs when

a bacteriophage packages a piece of bacterial DNA during replication

Hfr refers to

a cell in which the F plasmid has been integrated into the cell chromosome

During maturation or formation of phage particles,

a few phage heads may surround fragments of host bacterial DNA

The F pilus is

a protein appendage that attaches the two cells together

The classic transformation experiment done by Griffith used

harmless and virulent strains of Streptococcus pneumoniae

F+ cells

have a plasmid and are donors in conjugation.

Plasmids are

able to replicate independently of the chromosome.

The polymerase chain reaction uses DNA polymerase but not primase or helicase. Primase is usually responsible for

adding a short sequence of complementary RNA to the existing single DNA strand

The plasmid is mobilized for transfer when

an endonuclease cleaves it at the origin of transfer

The basic parts of a bacteriophage are

an icosohedral head, central tube, tail pins, and fibers

Mismatch repair is activated by

any difference between the nucleotide sequence in the donor and recipient DNAs.

A virus that infects bacterial cells is called a ______.

bacteriophage

The lac z gene codes for ______.

beta-galactosidase

Bacteria containing the plasmid shown in panel A would generate ______ colonies on medium containing x-gal, while those in panel B would generate ______ colonies

blue; white

After entry of the bacteriophage into the host cell, a phage enzyme

breaks the host into DNA fragments

The proofreading function of DNA polymerase reduces the error rate from about one in a million base pairs to about one in a ______ base pairs.

hundred million

The two strands of DNA are joined to each other or held together by

hydrogen bond

These dimers weaken ______ between bases.

hydrogen bonds

When the bacteriophage transfers bacterial DNA into a recipient bacterial cell, that DNA

can integrate into the chromosome

DNA polymerase:

can only add nucleotides to single-stranded DNA with a primer sequence

As a result of mismatch repair during transformation:

cells may have either original DNA or donor DNA in them

Scientists isolated a new species of bacteria growing in sediments collected from a 63 meter deep site at the bottom of Lake Washington in Seattle This species, named Labrys methylaminiphilus, is capable of obtaining its carbon and energy needs from methylamine (CH3NH2), a derivative of ammonia (NH3) in which one H atom is replaced by a methyl (CH3) group. L. methylaminiphilus grows at a temperature range of 10-35°C, with optimal growth at 28-30°C, and a pH range of 4.0-9.5, with optimal growth at 5.0-7.0. Because methylamine is a single carbon compound resulting from the breakdown of decaying organic matter, methylotrophic ("methyl-feeding") bacteria like L. methylaminiphilus play an important role in carbon cycling in lake sediments and other environments. Consider the growth of L. methylaminiphilus on methylamine. How would you classify this species based on its metabolism?

chemoorganoheterotroph

Cells that are capable of bringing DNA from their environment into the cell through their cell wall are ______.

competent

In addition to transformation, the other two forms of horizontal gene transfer are

conjugation and transduction

The first step in conjugation is

contact between the donor and recipient

UV light and other non-ionizing radiation damage DNA molecules by

creating thymine dimers between adjacent thymine nucleobases in the DNA chain.

The sample being tested in the polymerase chain reaction will be mixed with a primer, Taq polymerase, and ______.

deoxynucleotides

In the beginning of transformation, ______ binds to the target cell

double-stranded DNA

Transformation is a form of horizontal gene transfer that involves homologous recombination. Homologous recombination is

genetic recombination between similar or identical nucleotide sequences