Microbio Exam 3 (other tests) S-Test First

which of the following statements is false with respect to the basic strategy for cloning

host organism chromosomal dna is mutated by addition of chemical agent

which of the following is not a reason why plasmids are useful for the manipulation of dna

lack of restriction sites prevent unwanted cutting of plasmid by bacterial host

vehicles by which dna can be transported by the scientist/technician, and into which genes can be recombined and replicated

both cloning and expression vectors

m13mp18 contains and intergenic region modified by insertion of a polylinker, encoding 18 amino acids and containing multiple restriction sites with lacZ reporter. when used as a cloning vector, dna successfully inserted into the polylinker has which effect on bacterial cultures harboring m13mp18 grown on medium

colonies appear white

the sanger method of nucleotide sequencing relies on the addition of what type of molecule to terminate chain elongation

ddNTPs (limiting the reaction)

this type of molecule must be _____ in order for the procedure to work

limiting the reaction

the image at right shows a sequencing gel run using the sanger method. in the space provided, write the sequence of nucleotides indicated on the gel
for one extra point, indicate the correct sequence of the target (template) DNA used to perform the sanger sequencing method and label the 3' and 5' ends

CTAATGT
3' GATTACA 5' (answer)

the list below contains three methods used for the location or detection of a desired clone. the remaining methods in the list are generally not used for this purpose. circle the three correct ones

detection of protein function
antibody detection
nucleic acid probe

dna microarrays are used to perform which of the following analyses

determine which mRNA transcripts are present in a cell under a defined set of conditions

a common method for the identification of proteins is carried out by a process known as peptide mass fingerprinting. in the process the sequence of a protein is arrived at

by matching the gene sequences of theoretically digested gene products from the genome with predicted gene sequences from observed peptide masses of digested proteins

in two-dimensional gel electrophoresis, the separation of proteins is carried out in the first dimension based on the isoelectric point and in the second dimension based upon

size

the isoelectric point of a peptide is

the pH at which the charge of a peptide is 0

the types and proportions of fatty acids present in cytoplasmic membrane lipids and the outer membrane lipids of gram-negative bacteria are major phenotypic traits of interest. this technique is called 

FAME

• Fatty Acid Methyl Ester

which of the following statements is true? (assume bacterial genetics with no introns)

it is generally possible to determine the exact primary sequence of a protein if the genetic code for the protein is known

pyro-sequencing is a powerful technique for sequencing dna. which of the following is not true

existing nucleotides at the 3' end of the molecule are removed by heating

• Why: Pyrosequencing adds nucleotides, it does not remove them 

which of the following is a definition of the term paralogs as it relates to microbial genetics

two or more genes in the same cell whose similarity is the result of gene duplication within a chromosome

synthesis of an oligonucleotide with a sequence deviating in at least one base from the wild-type gene followed by replacement of the wild-type gene with the synthetic sequence is known as 

site-directed mutagenesis

the tac promoter is a chimeric promoter combining the -10 region of the lac operon and lac and the -35 region of the tryptophan operon trp

true

the tac promoter is often used in expression vectors. which of the following statements is true of the tac promoter

it is inducible with IPTG

• Why: The tac promoter is a hybrid promoter that is turned on when IPTG is added

FISH probes can be used to

differentiate taxonomic groups discriminate species with mixed bacterial populations

which is not a benefit of derived from living within a biofilm

competition between species is reduced

denaturation:
annealing:
extension:

90
50
70

what is being "annealed"

primer

for 5/6 of history, the dominant life form on earth has been unicellular

True

the principal evidence that supports the idea that rna was the nucleic acid from which all life evolved includes all of the following except

it is a common genetic material of viruses

• Why: Even though this is true, viruses need to infect cells and reproduce. This wont cut it

the miller urey experiment was responsible for which of the following

demonstrating that an electric spark, when applied to a mixture of presumed early earth gases, could produce many of the organic molecules found in living cells

The characteristics of mitochondria and chloroplasts that link them phylogenetically to the bacteria, has led scientists to theorize that early bacteria developed a relationship with proto-eukaryotes which has come to be known as the theory of

endosymbiosis

• Endo = inside

• Symbiosis = living together

the most plausible energy generating system to be used by the earliest cells on earth involves

anaerobic oxidation of H2 and reduction of S⁰

• Remember:

  • Earliest Earth = no oxygen (anaerobic) —> so the first cells could not use O₂

  • H₂ electron donor (gets oxidized)

  • S⁰ electron acceptor (gets reduced)

the uptake of an inorganic nutrient for use in biosynthesis is an example of

assimilative metabolism

the structure shown at the right is

phycobilin

in order to fix carbon using the Calvin Cycle, autotrophs require reducing power in the form of NAD(P)H + H+. this reducing power is necessary to

reduce 1,3 bisphosphoglyceric acid to glyceraldehyde 3-P

in cyclic photophosphorylation, which of the following is true?

ATP is produced, and NADPH is not produced, and O₂ is not produced

(# of carbons in final product)

calvin cycle:
hydroxypropionate pathway:
reverse citric acid cycle:

6

2

3

whether an organism is classified as a photoheterotroph or a photoautotroph depends on its

carbon source 

in the calvin cycle which of the following is true

12 molecuels of phosphoglyceric acid serve as carbon skeletons to for 6 new molecules of ribose bis-phosphate and 1 molecule of hexose

when electrons are forced backwards, against the thermodynamic gradient, to reduce NAD* to NADH, the process is known as

reverse electron transport

which of the following is not a characteristic of a microniche?

buffered against extreme changes in temperature

• Why: buffered is stable like for a macro-environment, micro-environments are constantly changing and are unstable

in microbiology, a population is always made up of members of a single species

True

in low nutrient environments bacteria are able to "tune down" metabolically and become smaller by undergoing _________, a process commonly associated with organisms in the open ocean

reductive cell division

the utilization of sulfur compounds as an energy source by chemolithotrophs typically leads to the acidification of surrounding waters. This is primarily due to:

the production of SO42- which in solution is protonated to form H2S04

• Sponge that grabs protons to make acidic water

viable non-culturable organisms make up the bulk of the microorganisms in
nature

true

the number of electrons involved in the complete oxidation of H2S to SO42- is:

8

because most microorganisms are difficult to grow in pure culture, the first step in isolating a microorganism from the environment is to grow it in a(n):

enrichment culture

what does the information provided in the chart below indicate about marine sulfate

not biological in origin

nitrogen cycle

NO₃, NO₂, NH₃

in hydrothermal vent communities, chemolithotrophic bacteria form the base of the food chain. these microorganisms derive energy from reduced sulfur, nitrogen and metal compounds as well as Hydrogen. What is the reservoir for the oxygen that is used by these microorganisms?
What is the reservoir for the reduced sulfur used by these organisms?

overlying seawater

hydrothermal vent water

In non-cyclic oxygenic photosynthesis, the primary electron donor is
electron acceptor

H₂O, NADP+

Sulfate reduction leads to the formation of which toxic gaseous compound?

H₂S

When trying to detect an auxotrophic mutant, it is possible to use a simple method of screening known as

Replica Plating

Transposition is a site specific recombination event that is mediated by the enzyme 

Transposase

In polymerase chain reaction, DNA is amplified following the rapid cycling of annealing, primer extension and denaturation steps. Match the temperature given below with the appropriate steps in PCR

Denaturation: 90 C

Annealing: 50 C

Primer Extension: 70 C

What is being annealed during the annealing step in PCR

Primers

A microinsertion or microdeletion of three bases immediately downstream from the start codon in a gene will have what effect upon the reading frame?

No effect

A point mutation which results in a change in the amino acid sequence of a protein is called a

Missense mutation

Which of the following statements is true? (Assume bacterial genetics with no introns answer one)

it is generally possible to determine the exact primary sequence of a protein if the genetic code for the protein is known

Fluorescent labeled antibody probes are most useful when

Looking for cells with a unique cell surface marker

True or False: Cloning Vectors are “vehicles” by which DNA is transported by the scientist/technician, into which genes can be recombined and replicated.

True

When a gene cassette is inserted into a wild-type gene, the gene function is disrupted. What type of mutant is produced?

Knockout Mutant

• Inserting a punch, you are knocking the person (gene) out

Which is NOT true about pyrosequencing?

Existing nucleotides at the 3’ end are removed by heating.

• pyro = fire/light, NOT removal

Sanger sequencing uses what type of molecule to terminate chain elongation?

ddNTPs

• dead end nucelotide

Synthesis of oligonucleotide with a sequence deviating in at least one base from the wild-type gene followed by replacement of the wild type gene with the synthetic sequence is known as:

Site-directed mutagenesis

• Directing the mutation to a site 

It is currently possible to determine the identity of every mRNA transcript produced under a single defined set of environmental conditions in a population of cells using a new and powerful technique. This new technique is based on the use of

DNA micro-arrays

• a RAY of thousands of glowing dots

Propionate is produced as a fermentation by-product; it is generated by the microorganism in large amounts and is relatively simple in structure. These characteristics identify propionate as a

Primary metabolite 

• Primary: normal, essential growth products 

Which of the following is not true of secondary metabolites?

A) Not essential for growth and reproduction
B) Often produced as a group of related compounds
C) Generally a product of energy metabolism
D) Formed at or near stationary phase

C) Generally a product of energy metabolism

• Specialty chemicals (anitbiotics, pigments), NOT energy prducts

True or False (circle one). The Escherichia coli genome is completely sequenced and the function of every gene is known

False

The natural transfer of gene(s) from one organism to another (often of different species) by any means other than fertilization is called

Horizontal gene transfer

• DNA pass little love letters horizontally (with genes in the letter ) so the teacher doesnt see it

A transducing phage is a

A virus that contains packaged bacterial DNA inside its capsid

• Delivery truck

Whether an organism is classified as a photoheterotroph or a photoautotroph depends on its _____

Carbon Source

• Light is shared — carbon decides the lifestyle

Chlorophyll is green because it

Absorbs red & blue light and reflects green light

The ultimate low light efficiency structure that functions like a solid state circuit and is found in the green sulfur bacteria and in Chloroflexus is known as the ________

Chlorosome

Which of the following are the two most common electron donors used by nitrifying bacteria? (circle two)

NH₄⁺ (ammonium)

NO₂⁻ (nitrite)

True or False (circle one). Formaldehyde is used in assimilatory reactions by methanotrophs

True

• Formaldehyde builds biomass

The reduction of NO₃⁻ to NO₂⁻ by an electron from the electron transport system used for the purpose of generating proton motive force to phosphorylate ATP is (dissimilative / assimilative) nitrate reduction. This is an (anaerobic / aerobic) process

Dissimilative

Anaerobic

• Dissimilative = Disposal —> waste product used for energy

• Nitrate reduction happens without O₂

Which of the following compounds is not energetically favorable for use as a terminal electron acceptor

Ferrous iron (Fe²⁺)

The characteristics of mitochondria and chloroplasts that link them phylogenetically to the bacteria, has led scientists to theorize that early bacteria developed a relationship with proto-eukaryotes which has come to be known as the theory of

Endosymbiosis

Name (any) one of the three most common products of denitrification

• NO

• N₂O

• N₂

a. Denitrification is good for sewage treatment because

b. Denitrification is bad for agriculture because

a. Bacterial and algal blooms are discouraged by denitrification

b. Assimilable nitrogen is consumed by the process of denitrification

Which of the following is not a benefit derived from living within a biofilm

A) Biofilms trap nutrients
B) Biofilms prevent detachment
C) Protected from reactive chemicals
D) Protected from grazing protists
E) Competition between species is reduced
F) Cells buffered from pH/temp/water/etc.

Competition between species is reduced

Which of the following statements is False?

A) Living microorganisms found in deep rock
B) Fresh-water microbes concentrated at surfaces
C) Lowest concentrations in open sea never below 10⁵ cells/ml
D) Updrafts can carry microbes to 20,000 feet
E) Deep-sea vent microbes are distantly related to terrestrial ones

Microorganisms in deep-sea vent communities have been shown to be only distantly related to microorganisms in other terrestrial habitats

Why is H₂S production more common in marine sediments than freshwater sediments (write it out)

Water has large amounts of sulfate

Two or more metabolically related populations are referred to as a:

Guild

In low nutrient environments bacteria are able to ‘tune down’ metabolically by undergoing __________, a process commonly associated with organisms in the open ocean

Reductive Cell Division

Cross-feeding in bacterial communities (for example: the oxidation of ammonia to nitrate by one organism, and the reduction of nitrate to ammonia by another) is referred to as

Syntropic consortia

Because most microorganisms are difficult to grow in pure culture, the first step in isolating a microorganism from the environment is to grow it in a(n)

Enriched Culture

Which of the following is not true of viable but non-culturable organisms?”

Options:
A) They are alive but can never be cultured
B) They do not grow in most standard media
C) They represent the majority of microorganisms isolated from the environment
D) They are most often detected by non-culture techniques

They are alive but can never be cultured

• They are not dead, just sleeping 

In performing 2-dimensional gel electrophoresis, separation of proteins in the first dimension is based upon differences in the isoelectric point (pI) of the protein. What is the definition of isoelectric point?

The point at which the net charge on the protein is zero

Which of the following is NOT a reason why plasmids are useful for the manipulation of DNA

Lack of restriction sites prevent unwanted cutting of plasmid by bacterial host

Bacteriophage M13 is suitable as a cloning vector for all of the following reasons, EXCEPT

It can alternate between lysogenic and lytic phases

A clone in the context of genetic engineering is

A strain of organism that carries a particular desired DNA sequence 

The list below contains three methods used for the location or detection of a desired clone. The remaining methods in the list are not generally used for this purpose. Circle each of the three correct methods below for the location or detection of a desired clone.

• Detection of protein function of the desired gene product

• Antibody detection of an expressed protein on the surface of a desired cell

• Detection of a particular gene sequence using a tagged nucleic acid probe

The Sanger method of nucleotide sequencing relies on the addition of what type of molecule to terminate chain elongation

ddNTP (limiting the reaction)

Pyro-sequencing is a powerful new technique for sequencing DNA. Which of the following characteristics is not true of pyro-sequencing?

Existing nucleotides at the 3′ end of the molecule are removed by heating

In the polymerase chain reaction, DNA is amplified following the rapid cycling of denaturation, primer extension and denaturation steps. Match the temperatures given below with the appropriate step in PCR (place the appropriate letter in the spaces provided):

• Denaturation → 90°C

• Annealing → 50°C

• Primer Extension → 70°C

It is currently possible to determine the identity of every mRNA transcript produced under a single defined set of environmental conditions in a population of cells using which technique from the following list?

DNA micro-arrays

The process of using restriction enzymes to cut out a segment of chromosomal DNA and replace it with a length of foreign DNA (often times containing an antibiotic resistance gene) is called:

Cassette mutagenesis

Synthesis of an oligonucleotide with a sequence deviating in at least one base from the wild-type gene followed by replacement of the wild-type gene with the synthetic sequence is known as:

Site directed mutagenesis

Which of the following is a definition of the term ‘Paralogs’ as it relates to microbial genomics?

Two or more genes in the same cell whose similarity is the result of gene duplication within a chromosome

In Two-Dimensional Gel Electrophoresis (2DPAGE), the identification of proteins is carried out by a process known as peptide mass fingerprinting. In this process the sequence of a protein is determined:

By matching gene sequences of theoretically digested gene products from the genome with predicted gene sequences from observed peptide masses of digested proteins

Which of the following is untrue of genetically engineered vaccines?

They take longer to develop and produce than attenuated vaccines

• They are faster and safe to produce (plug and play proteins)

True or False (circle one). The Escherichia coli genome is completely sequenced and the function of every gene is known

False