Bio Exam 2
Several investigators have estimated that around ________ genes are the minimum for a viable cell
250-300
Based on SSU rRNA phylogeny studies, the current scientific dogma is that there is/are __________ domains of life.
3
What is a suicide vector in molecular cloning?
A vector containing a gene that, when being expressed or selected for, kills the host. Only vectors that have been successfully inserted with the gene of interest can grow under selective conditions
The development of next-generation sequencing technologies resulted in:
A) a drastic decrease of sequencing costs. B) the advent of the "omics" era. C) the integration of bioinformatic tools to handle enormous amounts of sequence data. D) All answers are correct.
Which tool is required for generating phylogenetic trees?
All three tools are needed statistical analysis DNA sequencing Computers
Mitochondria in Eukarya originate from the uptake of a cell that was a predecessor of modern
Alphaproteobacteria.
This group of bacteria represents a genus of endospore-forming Firmicutes.
Bacillus
The domains of life defined by Carl Woese and based on genetic heredity are
Bacteria, Archaea, and Eukaryotes
Which genus of bacteria is a dominant commensal in the human gut?
Bacteroides
Which genus of bacteria is a predator attacking and killing other bacteria?
Bdellovibrio
How does the squid Euprymna scolopes, the Hawaiian Bobtail squid, control its bioluminescence?
By pumping most bacteria out of its light organ every morning.
After heterologous expression of your gene of interest as a protein and lysis of the recombinant E. coli cells you apply ______ order to separate large polymeric cell debris from the small soluble proteins.
Centrifugation
Which type of DNA uptake is dependent on a direct cell-to-cell transfer of a plasmid?
Conjugation
The only group of oxygenic phototrophic bacteria are the
Cyanobacteria
The template for RNA polymerase is ________, and the RNA chain growth is ________ the chain growth of DNA
DNA / identical to
All mutations during the replication of __________ happen randomly and spontaneously (assuming the absence of a chemical or physical mutagen).
DNA and RNA
Restriction enzymes recognize specific nucleotide sequences and cut them as part of a defense mechanism in bacteria. They are cutting
DNA double-strands.
The enzyme that covalently links both strands of a vector and inserted DNA in molecular cloning is
DNA ligase.
Match the steps in one "round" of PCR
Denature:95℃; double-stranded DNA becomes single-stranded Elongation: 72℃; taq DNA polymerase inserts nucleotides at 3'-end and produces PCR product Annealing: approximately 55℃; primers find complement region and bind to DNA
Which genera are sulfate-reducing bacteria?
Desulfovibrio and Desulfobacter
Which is the organism of choice as a host for most molecular cloning experiments?
Escherichia coli
Which of the following statements is true?
Eukaryotic genomes are composed mostly of noncoding DNA, whereas bacterial genomes have mostly coding DNA.
Most Archaea identified in anaerobic layers of soils and sediments are
Euryarchaeota.
Which of the following is NOT a possible "fate" of foreign DNA entering a bacterial cell?
Export of the DNA through the membrane and release to the exterior.
Archaea share traits with Bacteria, such as lacking a nucleus, having a circular chromosome, and possessing a peptidoglycan cell wall.
False
Horizontally transferred genes typically encode essential metabolic functions such as DNA replication, transcription, and translation.
False
Once you identify the phylum that a bacterium is phylogenetically related to you can deduce its metabolic strategy because metabolic characteristics are always the same in a given phylogenetic group
False
Which of the following is a disadvantage of a small viral genome?
Fewer viral proteins can be synthesized.
The reduction of N2 gas for use as a bioavailable source of nitrogen is called nitrogen
Fixation
Which technique separates DNA molecules based on size
Gel electrophoresis
A region of genetic information encoding a functional unit is called the
Gene
All of a cell's transcribed RNAs at a given time are collectively referred to as the cell's __________
Genome
Which of the following is least subject to change during sudden changes of environmental conditions?
Genome
What is a metagenome?
Genome sequences from all the organisms in a particular environment.
Which species of Epsilonproteobacteria is responsible for causing peptic ulcers in humans?
Helicobacter pylori
Mutations happen randomly in the chromosomes of all organisms, and those that ________ the fitness of the organism in a given environment will be retained in the lineage.
Increase
Viruses function as transduction agents in bacteria - one way of horizontal gene transfer - which ____ bacterial evolution.
Increases
The virulence genes of certain pathogens, such as Salmonella, are found condensed in genomic regions that are referred to as pathogenicity
Islands
Which of the following microorganisms is used in food and beverage industries?
Lactobacillus delbruckii b. Lactobacillus brevis c. All answers are correct. d. Propionibacterium sp. e. Saccharomyces cerevisiae
The majority of the diversity in the domain Eukarya is composed of
Microorganisms.
What can you say about the presence and distribution of viruses in a healthy human body?
Most viruses are bacteriophages, and reside in the large intestine.
Which of the following is NOT a palindrome? (Ignore punctuation).
Murder for a jar of red jam.
A particular organism converts NO3- to N2 during anaerobic respiration. In this case,
NO3- is an electron acceptor.
Which of the following is NOT only unique to certain lineages within the Archaea?
Proteins folded to enable increased heat stability
Molecular sequencing suggests that mitochondria arose from a group of bacterial organisms related to modern
Proteobacteria
Coronaviruses and poliovirus have in this in common: They are class IV viruses with a single strand (+) ________ genome and replicate in the animal cell's _______.
RNA / cytoplasm
Which of the following is NOT a consequence of carrying an RNA genome?
RNA viruses always carry a single-stranded RNA molecules, so they can never enter lysogeny and integrate into the host chromosome.
ll of the following groups are members of phytoplankton, but only _________ are a member of zooplankton.
Radiolaria
__________ naturally function to cut the DNA of invading bacteriophage and plasmid DNA at specific recognition sequences.
Restriction enzymes
Which genus of bacteria is very closely related to E. coli?
Salmonella
Which of the following is the best way to determine the species of a particular bacterium?
Sequence its DNA.
Over 500 distinct antibiotics were so far identified to be produced by this group of bacteriaOver 500 distinct antibiotics were so far identified to be produced by this group of bacteria
Streptomyces
_____________________are known to produce the typical earthy-smell compound geosmin, and a large variety of secondary metabolites, including a great diversity of antibiotics.
Streptomyces
A plasmid has been cut with a single-cut restriction enzyme (the plasmid has one recognition site for that enzyme), and now exhibits cohesive ends. What are possible reactions with these ends?
The ends can ligate to any DNA cut with the same restriction enzyme.
The work of Carl Woese enabled the establishment of a robust phylogenetic system based on DNA sequences. What did he work on?
The use of alignments and sequence comparison of the gene for the ribosomal ribosomal subunit.
The bacteriophages T4 and Mu are (1) _________________ viruses, while the influenza virus and HIV are (2)______________ viruses.
(1) DNA, (2) RNA
What is the approximate frequency of spontaneous mutation rate per base of a eukaryotic organism?
10 e-9
In seawater, viral particles outnumber bacterial and archaeal cells by about ______, and mainly consist of ________.
10-fold / bacteriophages
Members of this phytoplankton group are among the smallest in cell size, but when they reach high cell densities (bloom). After they die, their shell sinks to the bottom of the ocean, gets buried in the seafloor sediment, and when those deep layers from the past get pushed up they become visible, for example, as the White Cliffs of Dover, England.
coccolithophores
The process of active transport of DNA from a donor bacterium to recipient cells is known as __________
conjugation
A major group of marine phytoplankton that is essential to the marine food chain includes
dinoflagellates
Different members of this phytoplankton group are responsible for toxic "red ties", bioluminescent ocean waves at night, and the photosynthetic properties of coral tissue.
dinoflagellates
Most plasmids are
double-stranded DNA, though a few are not.
After digesting a DNA sequence, a restriction endonuclease leaves
either two blunt or two sticky ends.
Which category best describes E. coli?
facultative aerobe
All of the following are advantages of a small viral genome, except that
fewer viral proteins can be synthesized.
Diazotrophs are microorganisms that
fix atmospheric nitrogen (N2)
Bacteria have a generally __________ mutation rate than eukaryotes, and a _________ mutation rate than viruses.
higher / lower
Transduction is an example of
horizontal gene transfer.
Imagine you discover a bacterial species that contains folded invaginations of the cytoplasmic membrane and small intracellular carboxysomes. You assume from the presence of these structures that this bacterium
is capable of photosynthesis and autotrophy
Which metal is complexed in the center of the chlorophyll molecule?
magnesium (Mg)
Why can most organisms not grow at high temperatures?
membranes will stiffen DNA will unfold proteins will denature All these are consequences.
An organism capable of producing methane and from carbon dioxide and hydrogen performs a type of metabolism called __________ and, given its sources of electrons, it is a __________.
methanogenesis; lithotroph
There is a mutation that has changed the codon from UAC to UAA, which changes the translation from tyrosine to stop. Which type of mutation is this?
nonsense mutation
Redox balance is achieved in fermentation by ________ NADH back to NAD+, and _______ the organic intermediate.
oxidizing / reducing
For a given electron donor, the most energy will be released when oxygen serves as the final electron acceptor, because
oxygen is a stronger oxidizing agent than all other electron acceptors
The genes individual to each strain within a bacterial species is called the
pan genome
You have cloned your gene of interest into E. coli, which then express your gene - a small soluble cytoplasmic proteins. What is the correct order of recovering your protein from the cells?
pellet the cells - lyse the cells - pellet the cell debris - collect the supernatant - purify protein from the supernatant
The Z-scheme in oxygenic photosynthesis illustrates the electron transfer among
photosystem II and I.
Proofreading activity is intrinsic to the __________ enzyme to _________ the accumulation of mutations during a replicative cycle.
polymerase / minimize
The polymerase chain reaction has many cycles of three temperature steps: 95°C, ~55°C, and 72°C. At the ~55°C stage,
primers anneal to the denatured DNA strands.
Photoautotrophs use light to
produce ATP and reduce CO2.
Propionibacterium is used in the food industry for its
propionic acid fermentation - it produces the taste and holes in Swiss cheese.
A molecule of the group of __________ is used as a "molecular clock" to determine the approximate time since two lineages of organisms diverged.
rRNAs
The transfer of the F plasmid in E. coli from one donor cell to a __________ cell results in two __________ cells.
recipient / donor
The CRISPR system:
recognizes foreign DNA sequences that have previously entered the cell and directs the Cas proteins to destroy them.
All known microorganisms have a set of genes coding for __________, whose DNA sequences are highly conserved and thus are used for reconstructing phylogenetic trees.
ribosomal RNA
Once several different but related gene sequences have been obtained, which step must be performed BEFORE a phylogenetic tree can be constructed?
sequence alignment
The discovery of the CRISPR-Cas system in Bacteria fundamentally affected our understanding of virus-host interactions. This is system functions as
sequence-specific adaptive immunity of a bacterium against viruses.
Consider a mutation in which the change is from UAC to UAU. Both codons specify the amino acid tyrosine. Which type of point mutation is this?
silent mutation
You find that the 16S rRNA gene sequence of the bacterium you isolated differs by 3% from a group of known strains of bacteria. You conclude that your new bacterium is a new _____ within the same _____ with these strains.
species / genus
If a bacterial cell is competent, it means that
the bacterium can import free DNA fragments and incorporate it into its genome.
Which theory proposes an explanation for the origin of eukaryotic organelles?
the endosymbiotic theory
All of a cell's transcribed RNAs at a given time are collectively referred to as the cell's __________
transcriptome
Which of the following methods may introduce foreign DNA into a bacterial recipient?
transformation, transduction, and conjugation
When oxygen (O2) serves as the electron acceptor at the end of a respiratory electron transport chain, the product is
water
Which molecule is used for the analysis in a metagenomic study?
chromosomal and plasmid DNA
What mechanism allows the flu virus (influenza) to be so versatile, requiring us to get a new vaccination every "season", and the designed vaccines being in fact only a "best guess" to match the variability in the virus?
The virus has a high mutation rate in its genes encoding the surface H and N proteins (hemagglutinin and neuraminidase), so the composition of surface proteins changes quickly and the host immune system does not recognize the virus as a pathogen that it has previously encountered.
What are special characteristics among members of the phylum Firmicutes?
They can form endospores. They stain mainly Gram-positive. Both answers are correct
The entirety of RNA molecules produced during a given set of conditions is called a(n)
Transcriptome
The entirety of RNA produced under a given set of conditions is called a(n)
Transcriptome.
In ________, the number of genes transferred is limited by the size of the phage head.
Transduction
The process of importing free DNA into bacterial cells is known as:
Transformation.
The process of site-specific viral DNA integration into a bacterial chromosome is known as __________
Transposition
Antigenic shifts in the influenza genome generates hybrid viruses with strongly modified surface proteins, triggering new outbreaks of influenza after long periods of apparent immunity.
True
Bacteriophage Mu is a good tool for genetic manipulations because it replicates by transposition into a short, frequently occurring sequence, thereby generating a high frequency of mutations in the host cell chromosome.
True
Certain bacteria are able to obtain energy by fermentation of amino acids
True
If you want to clone and express a eukaryotic gene in bacteria, you need to have the matured mRNA sequence (without introns)
True
Microzooplankton are unicellular microbial eukaryotes that are the first consumers, also called grazers, in the marine carbon cycle.
True
Mutations happen naturally, or are induced by chemical or radiation treatment, and occur randomly at every site in the genome.
True
One important advantage of eukaryotic cells as hosts for cloning vectors is that they already possess the complex RNA and posttranslational processing systems required for the production of eukaryotic proteins.
True
Phages can be considered part of the human innate immune system because they can infect/kill bacteria entering our body that are potentially pathogenic to humans.
True
Restriction endonucleases are naturally occurring enzymes in bacteria to cleave foreign/viral DNA.
True
The domain Archaea does not contain any disease-causing organisms.
True
The quantity of energy released is low when the two half reactions' redox couples (their E0′) are relatively close to each other on the redox tower.
True
Thermophilic microbes usually contain heat-stable proteins that have a hydrophobic core and increased ionic groups on the outside:
True
You are investigating the microbial communities in a hot sulfur spring in Yellowstone National Park. You expect to find archaeal cell numbers and species diversity dominating proportionally over bacterial types.
True
Which gene is most likely to be encoded in the viral genome?
a gene for a capsid protein
Which of the following was likely the host cell during primary endosymbiosis?
a photosynthetic bacterium
A functional open reading frame (ORF) codes for
a protein.
Which statement is true?
a) All organisms have roughly the same DNA content. b) All organisms differ in DNA content, but contain roughly the same number of genes. c) All organisms differ in their genome size, and, their amount of genes.
Genetic engineering include laboratory techniques such as
a) nucleic acid hybridization. b) molecular cloning c) restriction enzyme digestion. d)All answers are correct
Fragments of nucleic acids can be separated based on their lengths using
agarose gel electrophoresis.
During genome assembly, you first have to __________, and then ________ .
align overlapping DNA fragments / ideally reconstruct the entire chromosome
When a genome is annotated, it means that
all genes in the genome have been located, and an attempt has been made to identify their individual functions.
Which lithotrophic metabolic strategy is most common in fertilized soil?
ammonia oxidation
X-gal is
an indole dye covalently bound to a sugar to mimic lactose, and a substrate for ß-galactosidase.
Methanogens in the natural environment require
associations with bacterial species
Besides fungi, which type of microorganism produces most of the known antibiotics?
bacteria of the actinomycete group
Some cyanobacteria contain carboxysomes. Carboxysomes are involved in
carbon dioxide fixation.
In purple bacteria, bacteriochlorophylls are supplemented by accessory pigments called:
carotenoids
Which of the following is an example of vertical gene transfer?
cell division
Which is a feature of fungi?
cell walls that contain chitin
Unicellular zooplankton are _________trophs, and are typically _________ than phytoplankton cells
chemoorgano / larger
