C8-C14 Flashcards
extracellular form of a virus
virion
protein shell of the virus
capsid
The virus redirects the host cell’s metabolism from growth to support virus replication and the assembly of new virions
virulent/ lytic infection
The host cell is not destroyed but is genetically altered
because the viral genome becomes part of the host genome.
lysogenic infection
Viral genomes of this configuration have the exact same base sequence as that of the viral mRNA that will be translated to form viral proteins.
plus configuration
Viral genomes of this configuration are complementary in base sequence to viral mRNA.
minus config
symmetry of rod-shaped viruses
helical symmetry
symmetry of spherical viruses
icosahedral symmetry
nucleic acid polymerases carried by RNA viruses that function to replicate the viral RNA genome and produce viral-specific mRNA
RNA dependent RNA polymerases- RNA replicases
example of enzyme carried by a virus that aid in their infection on the host cell
influenza virushas envelope proteins called neuraminidases that destroy glycoproteins and glycolipids of animal cell connective tissue, thus liberating the virions
carried by retroviral virions to make DNA from an RNA template
RdDp reverse transcriptase
viral life cycle
- Attachment (adsorption) of the virion to the host cell
- Penetration (entry, injection) of the virion nucleic acid into the
host cell - Synthesis of virus nucleic acid and protein by host cell machinery as redirected by the virus
- Assembly of capsids and packaging of viral genomes into new
virions - Release of new virions from the cell
number of virions release per cell
burst size
the number of infectious virions present per volume of fluid
titer
When a virus infects host cells growing on a flat surface, it creates a zone of cell lysis
plaque
efficiency of which virions infect host cells is rarely 100% and often considerably less. state reasons why
Virions that fail to infect may have assembled incompletely during the maturation process,
may contain defective genomes,
or may have suffered a spontaneous mutation that prevents them from attaching or otherwise properly replicating
example mechanisms of Archaea and bacteria against viral attack
toxin-antitoxin module
CRISPR
destruction of dsDNA through restriction endonucleases (process called restriction)
Besides encoding its own replication machinery, the T4 genome has another unusual feature: In a population of T4 virions, although each copy of the genome contains the same set of genes, they are arranged in a different order.
circular permutation
The T4 genome encodes three major
sets of proteins
early proteins, middle proteins, and late proteins
example of a virulent virus
Bacteriophage T4
some double-stranded DNA bacte rial viruses, although capable of a virulent cycle, can also infect
their host and establish a long-term stable relationship
temperate viruses
examples of temperate phages
lambda and P1
Maintenance of the lysogenic state is due to
phage encoded repressor protein
If lambda enters the lytic pathway, long, linear concatemers of genomic DNA are synthesized by a mechanism called
rolling circle replication
Instead of the lytic pathway, if lambda takes the lysogenic route, its genome integrates into the E. coli chromosome requiring a protein called
lambda integrase
Whether lysis or lysogeny occurs in a lambda infection depends in large part on the levels of two key repressor proteins that can accumulate in the cell following infection which are
lambda repressor, also called the cI protein, and a second repressor called Cro
it represses the transcription of
all other lambda-encoded genes, including Cro. When this happens, the lambda genome integrates into the host’s genome and
becomes a prophage
cI protein
represses expression of a protein called cII whose function is to activate the synthesis of cI. Hence,
following infection, if cI is present at insufficient levels to repress expression of phage-specific genes, this protein can accumulate in the cell; if this happens, lambda travels the lytic pathway
Cro
If an animal virus initially evades the immune system, animal viruses can catalyze at least four different outcomes
-A virulent infection results in lysis of the host cell; this is the most common outcome.
-a latent infection, the viral DNA exists in the host’s genome and virions are not produced; this leaves the host cell unharmed unless and until an event triggers the virulent pathway.
-With some enveloped animal viruses, release of virions, which occurs by a kind of budding process, may be slow, and the host cell may not be lysed (and thus not killed); instead it continues to grow and produce more virions. Such infections are called persistent infections.
-Finally, certain animal viruses can convert
a normal cell into a tumor cell, a process called transformation
structurally complex animal viruses that con tain an RNA genome. However, unlike other RNA viruses, the
genome is replicated inside the host cell by way of a DNA intermediate
retroviruses
Retroviruses are enveloped viruses and carry
several enzymes within the virion including
reverse transcriptase, integrase, and retroviral specific protease
the primary viruses
infecting prokaryotic cells
Double-stranded DNA viruses (class I)
the major viral predators of eukaryotic cells
single-stranded plus-sense RNA
viruses (class IV)
fungi are only infected by what class of viruses
Class III and IV
the vast majority of class I
viruses that infect eukaryotes replicate in what hosts
Animal hosts rather than plants
hosts of class II viruses
more plants rather than animals
host of class V
animals rather than plants
host of class VI
known only from animal hosts
class VII host
much more
common in plants than in animals
virus infecting the protozoan Acanthamoeba and
belongs to a group of giant viruses with large genomes called
nucleocytoplasmic large DNA viruses (NCLDV); multilayered and icosahedral capsid
mimivirus
comprise several virus families, including pox viruses, iridoviruses, and certain plant viruses. These viruses
share a set of highly homologous proteins, most of which function
in DNA metabolism.
NCLDV
ssDNA bacteriophage;has only a few genes and shows the phenomenon of
overlapping genes; contains a circular genome of 5386 nucleotides inside a tiny icosahedral virion, about 25 nm in diameter
Bacteriophage phiX174
ssDNA bacteriophage; a filamentous virus with helical symmetry; the
virion is long and thin and attaches to the pilus of its host cell; like other filamentous virus it has the unusual
property of being released from the host cell without the cell undergoing lysis;
Bacteriophage M13
dsDNA bacteriophage; a large, tailed, double-stranded DNA
virus of Escherichia coli that possesses complex morphology; kills it host; differs from many other bacteriophage genomes in that its DNA contains the modified cytosine base 5-hydroxymethylcytosine in place of cytosine; encodes its own DNA polymerase; although each copy of the genome contains the
same set of genes, they are arranged in a different order (circular permutation);
bacteriophage T4
When the T4 DNA is
packaged into capsids, the concatemer is not cut at a specific
sequence; instead linear segments of DNA just long enough to fill a
phage head are generated.
This is called headful packaging and is
common among bacteriophages.
dsDNA bacteriophage;a relatively small virulent DNA virus that infects
Escherichia coli and a few related enteric bacteria. The virion has an
icosahedral head and a very short tail; RNA polymerase recognizes only its gene promoters distributed
along the its genome; endonuclease cuts the concatemer at specific sequences thus, the DNA sequence in each virion is identical.
Bacteriophage T7
dsDNA bacteriophage; also infects Escherichia coli, is a
double-stranded DNA virus with a head and tail; a temperate bacteriophage
lambda
lambda regulation; represses the transcription of all
other lambda-encoded genes, including Cro. When this happens,
the lambda genome integrates into the host’s genome and becomes
a prophage
accumulation of cI
lambda regulation;represses expression of a protein called cII whose function is to activate the synthesis of cI. Hence, following infection, if
cI is present at insufficient levels to repress expression of phage specific genes, it accumulates in the cell; if this happens, lambda
travels the lytic pathway.
Cro
lambda regulation; function is to stabilize cII and protect it from
protease attack
cIII
DNA Archaeal viruses; virus morphology that commonly affects Euryarchaeota
head and tail type
DNA Archaeal viruses; The most morphologically distinctive archaeal viruses infect what phyla
hyperthermophilic Crenarchaeota
DNA Archaeal viruses; infects crenarchaeota; forms spindle-shaped virions that often
cluster in rosettes; also forms a rigid, helical rod-shaped structure
SSV, SIFV
DNA Archaeal viruses; forms a rigid, helical rod-shaped structure; A spindle-shaped virus that infects the hyperthermophile Acidianus displays a novel behavior. The virion contains a
circular genome of about 68 kilobase pairs and is lemon-shaped
when first released from the host cells. However, shortly after release
from its lysed host cell, the virion produces long, thin tails, one at
each end
ATV
DNA Archaeal viruses;A spindle-shaped virus also infects the hyperthermophile Pyrococcus (Euryarchaeota); resembles SSV but is
larger and contains a very short tail and do not have common evolutionary roots;
PAV1
ssDNA Archaeal viruses; infects the extreme halophile Halorubrum and is unusual not only
because of its circular single-stranded DNA genome but also due to its enveloped nonuniform
morphology
Pleomorphic virus 1 (HRPV-1)
ssDNA Archaeal viruses; infects the hyperthermophile Aeropyrum pernix . A filamentous capsid surrounds this circular single stranded 24.9-kilobase viral genome, which is double the size of the second largest known single-stranded DNA viral genome.
Aeropyrum coil-shaped
virus (ACV)
archaea unique method of viral release; their genomes encode structural proteins for their capsids, they also encode a protein called PVAP (protein forming virus-associated pyramid) that facilitates viral release from the cell. PVAP assembles into seven-fold pyramid structures that rupture the host cell’s S-layer and open outwards to create a portal for viruses to exit the host cell.
S. islandicus rod-shaped
virus 2 (SIRV2) and turreted icosahedral virus (STIV)
uniquely replicating DNA animal virus; first virus to be studied in any detail and was
the first virus for which a vaccine was developed; among the
largest of all viruses, the brick-shaped vaccinia virions measuring
almost 400 nm in diameter; replication occurs in cytoplasm
pox virus
uniquely replicating DNA animal virus; group of small and naked icosahedral viruses that contain linear double-stranded DNA genomes; Attached to the 5′ end of the genomic DNA is a protein called the adenoviral terminal protein, and it is essential for replication of the genome. The complementary DNA strands also have inverted terminal repeats that play a role in the replication
process; of minor health importance, causing mild respiratory infections in humans; dsDNA is replicated without the formation of a lagging strand
adenoviruses
DNA tumor viruses; naked icosahedral virus that can cause
tumors in small mammals, such as hamsters and rats. Its circular
genome consists of double-stranded DNA; genome is too small (5.2 kb) to encode its own DNA polymerase,
so host DNA polymerases are used and DNA is replicated in a bidirectional fashion from a single origin of replication; When SV40 infects a host cell, one of two outcomes can occur, In permissive hosts, virus infection results in the usual formation of new virions and the lysis of the host cell.
In nonpermissive hosts, lytic events do not occur; instead, the viral DNA becomes integrated into host DNA, genetically altering the
cells in the process; allowing cells to be malignant; transcription of the viral genome occurs in nucleus
Polyomavirus SV40
DNA tumor viruses; a large group of double-stranded DNA viruses that cause a variety of human diseases, including fever blisters (cold sores), venereal herpes, chicken pox, shingles, and infectious mononucleosis; examples- Epstein–Barr virus causes Burkitt’s lymphoma, CMV; remain latent in the body for long periods and become active under conditions of stress or when the
immune system is compromised; enveloped; replication in the nucleus
Herpesviruses
pos strand RNA viruses; The virus infects cells of Escherichia coli by attaching to
the cell’s pilus; encodes only four proteins, including the maturation protein, coat protein, lysis protein, and one subunit of RNA replicase, the enzyme that replicates
the viral RNA
Bacteriophage MS2
pos strand RNA viruses; one of the smallest of all viruses; genome (about 7.4 kb) is also the
mRNA, and the VPg protein facilitates binding of the RNA to host ribosomes; replication in host cell cytoplasm
poliovirus
pos strand RNA viruses; single-stranded plus RNA viruses that; replicate in the cytoplasm; cause respiratory infections in humans and other animals, including about 15% of common colds; enveloped and contain club-shaped glycoprotein spikes on their surfaces; the largest of
any known RNA viruses, about 30 kb; virions are assembled within the
Golgi complex,
coronaviruses
neg strand RNA Animal Virus; causes the fatal neuroinflammatory disease rabies ;is a rhabdovirus (rod-shaped); genome transcribed by replicase in the cytoplasm; with nucleocapsid and envelope
rabies virus
neg strand RNA Animal Virus; an enveloped virus in which the viral
genome is present in the virion in a number of separate pieces, a
condition called a segmented genome (8 linear single stranded molecules; pleiomorphic due to budding; with hemagglutinin and neuraminidase; also rna replicase and rna endonuclease; exhibits antigenic shift in which segments of the RNA genome from two different strains of the virus infecting the same cell are reassorted generating hybrids that express unique surface proteins unrecognized by the immune system
influenza virus
dsRNA virus; a typical reovirus and is the most common cause of
diarrhea in infants 6 to 24 months of age; segmented genome
rotavirus
dsRNA virus; replication occurs exclusively in the host cytoplasm but
within the nucleocapsid itself; RNA replication is conservative as only the minus strand is a template in the infecting nucleocapsids, whereas only the plus strand is a template in the synthesis of double-stranded genomic RNA from assimilated plus-strand RNA copies in progeny virions
reovirus
viruses that uses reverse transcriptase; have enveloped virions that contain two identical copies of the single-stranded plus complementarity RNA genome; name refers to the fact that
these viruses transfer information from
RNA to DNA; To begin the
process, the genome is converted to DNA
by reverse transcriptase inside the
nucleocapsid and then the DNA is
released to the cytoplasm
retrovirus; HIV
viruses that uses reverse transcriptase; tiny DNA genomes re unusual because they are neither
single-stranded nor double-stranded; instead, they are partially
double-stranded.
hepadnaviruses; HBV
subviral agents; are infectious RNA molecules that lack a protein component; small, circular, single-stranded RNA molecules that
are the smallest known pathogens; cause a number of important plant diseases and can
have a severe agricultural impact(ie coconut cadang-cadang viroid); infects plants; known to yield
small interfering RNAs (siRNAs) as a by-product of replication
viroids
subviral agents; infectious agents whose extracellular form consists entirely of
protein; lacks both DNA and RNA; cause several neurological diseases such as scrapie in sheep, bovine spongiform encephalopathy (BSE or “mad cow disease”) in cattle, chronic wasting disease in deer and elk. and kuru and variant Creutzfeldt–Jakob disease in humans by catalyzing protein conformational changes that lead to protein clumping and accumulation; none in plants some in yeasts; forms amyloids;
prions
subviral agents; nonpathogenic prions; a protein that regulates the transcription of genes encoding certain nitrogen metabolism functions
[URE3] prion
subviral agents; nonpathogenic prions; s a human protein that
is part of our innate immune system and has been shown to convert to a self-perpetuating prion-like form in cells that become infected with a virus. its aggregation triggers the production of immune modulators called interferons;
MAVS protein
valuable tools to visualize the localization of specific proteins and to monitor gene
expression in cells
reporter genes
encode proteins that are easy to detect or assay and are used by fusing
them to genes of interest in such a way that both the reporter gene
and the gene of interest are coexpressed
reporter genes
For visualizing molecular
events, reporter genes that encode fluorescent products such as the
green fluorescent protein (GFP)
leads to
unwinding of the DNA and loading of the replisome for chromosome replication in Escherichia coli
binding of DnaA to specific DNA
sequences within the oriC region of the chromosome
one of several penicillin-binding proteins present in the cell.
FtsI
ensures the divisome forms only at the center and not at the cell poles
Min proteins (MinC, MinD, MinE)
controls the assembly site of FtsZ in Caulobacter
MipZ ( midcell positioning of FtsZ)
The major shape-determining factor in Bacteria is the protein
MreB
Inactivation of
the gene encoding MreB or other proteins in the elongasome leads
rod-shaped bacteria to become coccus-shaped.
In the vibrio-shaped bacterium Caulobacter, a shape-determining
protein is present in addition to MreB called
crescentin
a plant pathogen,
elongates at one pole in a process called unipolar elongation
Agrobacterium tumefaciens
insertion of new peptdidoglycan; plays a major role in the simultaneous insertion of peptidoglycan precursors.
bactoprenol
insertion of new peptdidoglycan; a hydrophobic C55 alcohol that is
bonded to an N-acetylglucosamine/N-acetylmuramic acid/
pentapeptide peptidoglycan precursor to form lipid II
bactoprenol
insertion of new peptdidoglycan; ??? transports peptidoglycan precursors across the cytoplasmic membrane by rendering lipid II sufficiently hydrophobic
to pass through a transmembrane ABC transporter known as ???
bactoprenol, flippase
insertion of new peptdidoglycan; lipid II interacts with peptidoglycan polymerases called ??? that insert peptidoglycan precursors
into a growing point in the cell wall and catalyze glycosidic bond
formation (the remaining bactoprenol is then recycled to the cytoplasm to begin a new round of
precursor transport)
transglycosylases
insertion of new peptdidoglycan; prior to insertion of the peptidoglycan precursor, small gaps in the existing peptidoglycan are made by enzymes called; enzymes that function to hydrolyze the bond that connects
N-acetylglucosamine with N-acetylmuramic acid in the peptidoglycan backbone.
autolysins
insertion of new peptdidoglycan; final step in peptidoglycan synthesis; forms the peptide cross-links between muramic acid residues in adjacent glycan chains
transpeptidation
Endospore formation sporulation factors; When highly
phosphorylated, sporulation proceeds; controls the expression of several sporulation-specific genes
Spo0A
Triggers for Activating Endospore Germination; receptors present in the endospore
germinant receptors (GRs)
Triggers for Activating Endospore Germination; GRs in a cluster which functions to sense and bind nutrients such as amino acids, sugars, and cell wall peptides from vegetative cells.
germinosome
Triggers for Activating Endospore Germination; next step to spore germination after stage I
triggering of cortex lytic enzymes (CLE) to degrade peptidoglycan in the endospore cortex,
Triggers for Activating Endospore Germination; modified from normal peptidoglycan such that CLE can recognize it and
not degrade cell wall peptidoglycan produced during outgrowth of
vegetative cells.
cortex peptidoglycan
Triggers for Activating Endospore Germination; major event of stage II- germination
removal of he endospore cortex
Triggers for Activating Endospore Germination ; triggered by the increased expression of genes encoding enzymes that biosynthesize peptidoglycan, teichoic acid and lipoteichoic acids, and the cell division protein FtsZ
stage III- outgrowth
Caulobacter Differentiation; three major regulatory
proteins whose concentrations oscillate in succession.
GcrA, CtrA, DnaA
Caulobacter Differentiation; the transcriptional regulators
GcrA and CtrA
Caulobacter Differentiation;a protein that functions both in its normal role in initiating DNA
replication and also as a transcriptional regulator
DnaA
Anabaena heterocyst; The cascade of events leading to heterocyst formation is triggered by
a limitation of “fixed” nitrogen (nitrate, ammonia, etc.)
Anabaena heterocyst; limitation of “fixed” nitrogen (nitrate, ammonia, etc.) is sensed in the vegetative cell as an elevation in levels of
???? , the acceptor molecule for formation of the amino
acid glutamate
a-ketoglutarate
Anabaena heterocyst; the major transcriptional regulator controlling heterocyst formation
HetR
Biofilm formation; The actual switch from planktonic to
biofilm growth in many bacteria is triggered by the cellular accumulation of the regulatory nucleotide
cyclic di-guanosine monophosphate
(c-di-GMP)
Biofilm formation; a classic opportunistic pathogen and from its primary reservoir in soil can infect the blood, lungs, urinary tract, ears, skin, and
other tissues of humans; causes The major symptoms of the human genetic
disease cystic fibrosis; form a tenacious biofilm
containing specific polysaccharides that subsequently increase its
pathogenicity and prevent the penetration of antibiotics
Pseudomonas aeruginosa
Biofilm formation; regulatory molecules
acyl homoserine lactones (AHLs)
Biofilm formation; Elevated c-di-GMP levels initiate the production of EPS, including
a polysaccharide called which functions as both a primary scaffold for the microbial community and a mechanism for resisting
the penetration of antibiotics
Pel
Biofilm formation; archaea that forms biofilm
motile
hyperthermophilic sulfur chemolithotroph Sulfolobus acidocaldarius
Antibiotics; target DNA gyrase in gram-negative bacteria and topoisomerase IV in gram-positive bacteria; lead to cell death by interfering with DNA unwinding
and replication
quinolones such as ciprofloxacin
Antibiotics; prevent RNA synthesis by either blocking the RNA polymerase active
site or blocking RNA elongation by binding to the major
groove in DNA
rifampin and actinomycin
Antibiotics; contains a region that mimics the 3′ end of a
tRNA, and this structural mimicry results in specific binding of the antibiotic to the A site in the 70S ribosome; this induces chain termination
and effectively shuts down protein synthesis.
puromycin
Antibiotics; specifically target the 16S rRNA of the 30S
ribosome and result in the ribosome misreading mRNAs, thus leading
to error-filled proteins that accumulate in the cell and ultimately inhibit
growth.
Aminoglycoside antibiotics such as streptomycin
Antibiotics; a lipopeptide produced by certain Streptomyces species that specifically binds to phosphatidylglycerol residues of the
bacterial cytoplasmic membrane; this leads to pore
formation and depolarization of the membrane, ultimately resulting in cell death.
Daptomycin
Antibiotics; cyclic peptides whose long hydrophobic tails specifically target the
LPS layer and ultimately disrupt membrane structure, causing leakage and cell death. (gneg)
polymyxins
Antibiotics; target the synthesis of peptidoglycan in bacteria; inhibit growth by interfering with proteins
that catalyze transpeptidation
b-lactams penicillin, cephalosporin, and their derivatives
Antibiotics; inhibits
peptidoglycan synthesis in gram-positive bacteria by binding to the
pentapeptide of peptidoglycan precursors and preventing the formation of peptide interbridges by transpeptidases.
vancomycin
Antibiotics; prevents peptidoglycan synthesis by binding to the peptidoglycan precursor transport system (bactoprenol) and
preventing new peptidoglycan precursors from reaching the site
of peptidoglycan synthesis. As autolysins continue to introduce
small gaps in the existing peptidoglycan, a shortage
of precursors to patch the gaps weakens the cell wall and leads to
cell lysis
topical antibiotic
bacitracin
bacterial resistance mechanisms to antibiotics
(1) modification of the drug target,
(2) enzymatic inactivation,
(3) removal from the cell via efflux pumps, and
(4) metabolic bypasses
exhibits antibiotic resistance by producing an alternative penicillin-binding protein called MecA that is unaffected by methicillin or other b-lactam antibiotics.
Methicillin-resistant Staphylococcus aureus
mechanisms behind MRSA
presence of the Staphylococcus chromosomal cassette for methicillin resistance (SCCmec) containing the gene for MecA, which is activated in the presence of methicillin or other b-lactam antibiotics antibiotics through a regulatory mechanism involving MecI and MecR1 proteins.
eoccurs when a population of antibiotic-sensitive bacteria produces rare cells that transiently become tolerant to multiple antibiotics
persistence
genes that encode two components: a toxin whose production inhibits cell growth and an antitoxin that counteracts the activity of the toxin.
Toxin–antitoxin (TA) modules
encode a TA module that has been shown to trigger
persistence in E. coli
hipAB genes; HipA is a toxin
that inhibits translation and HipB is an antitoxin that is susceptible
to a protease called Lon.
a heritable
change in the base sequence of that genome, that is, a change that
is passed from the mother cell to progeny cells
mutation
a strain
of an organism or a virus isolated from nature is called the
wild-typestrain
A
cell or virus derived from the wild type whose genome carries
achange in nucleotide sequence is called a
mutant
A mutant by
definition differs from the wild-type strain in its
genotype
nutritionally defective
mutants can be detected by the technique of
replica plating
A mutant strain with an additional nutritional requirement
above that of the wild type or parental strain from which it was
derived is called an
auxotroph
the strain from
which an auxotroph originates is called a
prototroph
mutations that occur without external intervention, and most result from occasional errors in the pairing of
bases by DNA polymerase during DNA replication
spontaneous mutation
mutations that are e caused by environmental agents and include mutations made deliberately by humans.
induced mutations
Mutations that change only one base pair and occur when a single base-pair substitution occurs in the DNA
point mutations
a change in the RNA from UAC to UAU
would have no apparent effect because UAU is also a tyrosine codon. Although they do not affect the sequence of the encoded polypeptide,
such changes in the DNA are considered one type of mutation,
that is, a mutation that does not affect the phenotype of the cell.
silent mutation
a single base change from UAC to AAC results in an amino acid change within the polypeptide from tyrosine to asparagine at a specific site; the informational “sense” (the precise sequence
of amino acids) in the polypeptide has changed. this is called a
missense mutation
Another possible outcome of a base-pair substitution is the formation of a stop codon in the DNA. This results in prematture termination of translation, leading to an incomplete
polypeptide
nonsense mutation
are mutations in which one purine base (A or G) is substituted for
another purine, or one pyrimidine base (C or T) is substituted for another pyrimidine
transitions
point mutations in which a
purine base is substituted for a pyrimidine base, or vice versa.
transversions
any deletion or
insertion of a single base pair results in a shift in the reading
frame; often have serious consequences
frameshift mutations
many
large insertion mutations are due to the insertion of specific DNA
sequences called
transposable elements
Point mutations are typically reversible, a process known as
reversion
a strain in which the original phenotype that was changed by mutation is restored by a second mutation.
revertant
the mutation that restores activity is at the same
site as the original mutation
same-site revertants
If the back mutation is not only at the
same site but also restores the original sequence, it is called a
true revertant
the mutation is at a different site in the
DNA; can restore a wild-type phenotype if they function as suppressor mutations—mutations that compensate
for the effect of the original mutation
second-site revertants
class of suppressor mutations
(1) a mutation somewhere else
in the same gene that restores enzyme function, such as a second
frameshift mutation near the first that restores the original reading
frame ;
(2) a mutation in another gene that restores the
function of the original mutated gene; and
(3) a mutation in another
gene that results in the production of an enzyme that can replace
the nonfunctional one.
For most microorganisms, errors in DNA replication occur at a frequency of
10-6 to 10-7
per thousand bases during a single round
of replication
Single base errors during DNA replication are more likely to lead
to missense mutations than to nonsense mutations because
most
single base substitutions yield codons that encode other amino acids
a variety of chemical, physical, and biological agents that can increase the mutation rate
and are therefore said to induce mutations.
mutagens
molecules that resemble the
purine and pyrimidine bases of DNA in structure but display faulty
base-pairing properties; DNA may replicate normally most of the time however, DNA replication errors occur at
higher frequencies at these sites due to incorrect base pairing. The
result is the incorporation of a mismatched base into the new strand
of DNA and thus introduction of a mutation; mutation is revealed during the subsequent segregation of this strand in cell division
nucleotide base analogs
powerful mutagens
and generally induce mutations at higher frequency than base analogs; chemical mutagens induce chemical modifications in one
base or another, resulting in faulty base pairing or related changes
alkylating agents (chemicals that react
with amino, carboxyl, and hydroxyl groups by substituting them
with alkyl groups) such as nitrosoguanidine
chemical mutagens; are planar
molecules that function as intercalating agents; inserted between two DNA base pairs and push them apart.
Then, during replication, this abnormal conformation can trigger single base insertions or deletions. Thus, typically induce
frameshift rather than point mutations; Ethidium bromide
acridines
e two forms of electromagnetic radiation that are highly mutagenic
Nonionizing and ionizing radiation
widely used to generate mutations because the
purine and pyrimidine bases of nucleic acids absorb UV radiation
strongly (the absorption maximum for DNA and RNA is at 260nm).
The primary mutagenic effect is the production of pyrimidine dimers,
in which two adjacent pyrimidine bases (cytosine or thymine) on the same strand of DNA become covalently bonded to one another
UV radiation
These rays cause water and other substances to ionize, resulting in
the formation of free radicals such as the hydroxyl radical that can damage macromolecules in the cell,
including DNA. This causes double-stranded and single-stranded
breaks that may lead to rearrangements or large deletions.
ionizing radiation x-rays, cosmic rays, gamma rays
system initiates a number of DNA
repair processes, some of which are error-free; also allows DNA repair to occur without a template, that is,
with random incorporation of nucleotide precursors (deoxyribonucleotide triphosphates
[dNTPs]);
results in many errors and hence many mutations; mutations induced are better than the alternative (death of the cell), as mutations can often be corrected while
chromosome breaks usually cannot.
SOS repair system
In DNA damage tolerance, DNA lesions remain in the
DNA, but are bypassed by specialized DNA polymerases that can
move past DNA damage—a process
translesion synthesis
In E. coli, in which the process of mutagenesis has been studied in great detail, the two error-prone repair polymerases are
DNA
polymerase V, an enzyme encoded by the umuCD genes, and
DNA
polymerase IV, encoded by dinB
Both are induced as
part of the SOS repair system
The master regulators of the SOS system are the proteins
LexA and
RecA.
SOS repair system; a repressor that normally prevents expression of the SOS system.
LexA
SOS repair system; normally functions in genetic recombination , is activated by the presence of DNA damage, in particular by the single-stranded DNA that results when replication stalls.
RecA
It should be noted that DNA transfer typically occurs in
only one direction, from
donor to recipient
DNA that
enters the cell by horizontal gene transfer faces three possible fates:
(1) It may be degraded by the recipient cell’s restriction enzymes or other DNA destruction systems (2) it may replicate by itself (but only if it possesses its own origin of replication, such as a plasmid or phage genome); or
(3) it may recombine with the recipient cell’s chromosome.
is the physical exchange of DNA between genetic
elements (structures that carry genetic information).
recombination
This type
of recombination is often essential to a cell’s ability to retain DNA
following genetic exchange and is behind the well-known phenomenon of “crossing over” in the genetics of eukaryotes.
homologous recombination
key to homologous
recombination.
RecA protein (SOS repair system)
if a copy
of the wild-type gene is introduced into the same cell on a plasmid
or viral genome, this gene will encode the necessary protein and,
assuming the gene is transcribed and translated, will restore the
wild-type phenotype. This process is called
complementation because the wild-type gene is said to complement the mutation, in this case
converting the Trp- cell into Trp+
DNA derived
from virtually any portion of the host genome is packaged inside
the mature virion in place of the virus genome.
generalized transduction
DNA from a specific region of the host chromosome is integrated directly into the virus genome—usually
replacing some of the virus genes. This occurs only with certain temperate viruses such as phage lambda
specialized transduction
during lytic infection, the enzymes responsible for packaging viral DNA into the
bacteriophage sometimes package host DNA accidentally. The result
is called a
transducing particle
allows the transfer of any gene from one
bacterium to another, but at a low frequency.
Generalized transduction
allows extremely efficient transfer but is selective and
transfers only a small region of the bacterial chromosome
specialized
transduction
Alteration of the phenotype of a host cell by lysogenization is called
phage conversion
are the
result of prokaryotic cells hijacking defective viruses and using them
specifically for DNA exchange; defective bacteriophages
gene transfer agents (GTAs)
The
F plasmid is actually an episome, a plasmid that
can integrate into
the host chromosome.
Cells possessing a nonintegrated F plasmid are called
F+
F plasmid integrated into the chromosome are called
Hfr
Overall, the presence of the F plasmid results in three distinct
changes in a cell:
(1) the ability to synthesize the F pilus
(2) the mobilization of DNA for transfer to another cell, and
(3) the alteration of surface receptors so the cell can no longer be a recipient
in conjugation and is therefore unable to take up a second copy of
the F plasmid or any genetically related plasmids.
F plasmids containing chromosomal genes are called
F′ (F-prime) plasmids.
used to inhibit growth of
extreme halophiles,
novobiocin (a DNA gyrase inhibitor) and mevinolin (an inhibitor of
isoprenoid biosynthesis)
inhibit methanogens
puromycin and neomycin (both protein synthesis inhibitors)
mimics a virus because the genetic
element encodes a portion of a structurally defined particle that
transfers the plasmid between Halorubrum lacusprofundi strains.
pR1SE
Only one archaeal virus, which infects the thermophilic methanogen ???, has been
shown to transduce host genes.
Methanothermobacter thermautotrophicus
stretches of DNA that can move from one site
to another.
transposable elements
The two major types of transposable elements in Bacteria are
insertion sequences (ISs) and transposons
the simplest type of transposable
element. They are short DNA segments, about 1000 nucleotides
long, and typically contain inverted repeats of 10–50 base pairs.
insertion sequences (IS)
larger than IS elements but have the same two
essential components: inverted repeats at both ends and a gene
encoding the transposase
transposons
transposon which encodes resistance to the antibiotics
kanamycin (and neomycin), streptomycin, and bleomycin
transposon Tn5
transposon which encodes tetracycline resistance.
Tn10
Two mechanisms of transposition are known:
conservative and
replicative
as occurs
with the transposon Tn5 , the transposon is excised
from one location and reinserted at a second location. The copy number of a conservative transposon therefore remains at one
conservative transposition
a new copy of the transposon is produced and inserted at the second location. Thus, after
this transposition event, one copy of the transposon
remains at the original site, while a second copy is incorporated at
the new site.
replicative transposition
A major antiviral defense system present in both Bacteria and
Archaea is ??? which functions to seek out and destroy foreign
nucleic acid.
CRISPR—clustered regularly interspaced short palindromic repeats
These proteins possess endonuclease activity and both mediate the defense
against foreign DNA and incorporate new spacers into the CRISPR
region.
Cas proteins (CRISPR- associated)
correspond to
sequences of viral or other foreign DNA and function as a “memory
bank” of past encounters with a virus in a manner reminiscent of
how animals produce antibodies and long-lasting memory cells against and infecting virus; alternate with CRISPR regions are short repeats of constant DNA sequence present on the host chromosome
spacers
the first ammonia-oxidizing (nitrifying)
archaeon known,
Nitrosopumilus,
refers to the use of computers to
store and analyze the sequences and structures of nucleic acids and
proteins
bioinformatics
refers to the use of computers to
store and analyze the sequences and structures of nucleic acids and
proteins
dideoxy
method developed by the British scientist Fred Sanger
second-generation sequencing method still widely used
today, is based on the Sanger method and employs the light-emitting
enzyme luciferase to detect incorporation of dNTPs by emitting a pulse of light
pyrosequencing
in Bacteria, translation begins at start codons located immediately downstream of a ribosome-binding
sequence (RBS ) on the mRNA also known as
Shine–Dalgarno site
some codons are used more frequently than others. The is known as
codon bias
is the science that analyzes pooled DNA or RNA from an environmental sample containing organisms that have not been isolated and identified
metagenomics
Just as the total gene content of an organism is its
genome, so the total gene content of a microbial community is its
metagenome
When DNA is
denatured (that is, the two strands are separated), the single
strands can form hybrid double-stranded molecules with other
nucleic acid molecules by complementary or almost complementary base pairing
hybridization
The single-stranded segments of nucleic acid,
whose identity is already known, are called
nucleic acid probes
The genome-wide study of the structure, function, and activity of an
organism’s proteins is called
proteomics
is an advanced
version of mass spectrometry that does not require the protein separation and digestion step; Instead the sample is affixed
to a matrix and then ionized and vaporized by a laser
MALDI (matrix-assisted laser desorption ionization)
ons produced in MALDI are accelerated towards the detector by an electric field, where the time of flight (TOF) of each ion is measured. The smaller the mass/charge ratio of an ion, the faster it moves. The detector records the TOF of each ion, allowing the computer to calculate the mass and molecular formula.
MALDI-TOF
a more useful technique that can directly analyze
biological samples without the need for special analytical preparation;a laser is used to ionize the samplebut the silicon-coated surface used in NIMS
does not generate the background interference seen during ionization of a matrix by MALDI-TOF
nanostructure-initiator mass spectrometry (NIMS)
critical for studyingthe
metabolic potential of microorganisms in natural microbial communities
single-cell genomics (SCG)
Sequencing DNA from single cells relies on a modified version
of the polymerase chain reaction called
multiple displacement amplification (MDA)
refers to the use of in vitro techniques to alter genes in the laboratory.
Genetic engineering
Taq polymerase, a DNA polymerase isolated from
the thermophilic hot spring bacterium is stable to 95°C and thus is unaffected by the denaturation step employed in the PCR
Thermus aquaticus
A DNA polymerase , Pfu polymerase, from a hyperthermophilic species of
Archaea with a growth temperature optimum of 100°C; more thermostable than taq; has proofreading activity
Pyrococcus furiosus
a technique
that employs an agarose gel to separate nucleic acid fragments based
on differences in their size and charge
gel electropheresis
f nucleic acid fragments of known sizes
ladder
Single-stranded nucleic
acids whose identity is already known and that are used in hybridization are called
nucleic acid probes
When DNA is denatured, the single strands can be used to form
hybrid double-stranded molecules with other single-stranded DNA
(or RNA) molecules by complementary base pairing
in a process called
nucleic acid hybridization
probes of
known sequence are hybridized to target DNA fragments that have
been separated by gel electrophoresis. The hybridization procedure
in which DNA is the target sequence in the gel, and RNA or DNA is
the probe, is called a
southern blotting
uses RNA as the target sequence and DNA or RNA as the probe to
detect gene expression.
northern blotting
approach allows the identification of pathogens in clinical samples
or bacteria of interest in environmental samples
fluorescence in situ hybridization (FISH) technique
The movement of desired genes from their original source to a small
and manipulable genetic element (the vector) is called
molecular cloning
The cell is protected from its own restriction enzyme(s) by
hemical modification (typically by methylation)
of one of the bases in any potential restriction sites that exist in its
genome
This restriction enzyme makes staggered cuts, leaving
short, single-stranded overhangs called “sticky” ends at the termini of
the two fragments
EcoRI
This restriction enzyme cut both
strands of the DNA directly opposite each other, resulting in blunt
ends
EcoRV
an enzyme that covalently links the strands of
the vector and the source DNA; If the source
DNA is PCR generated, it is used to join the amplified DNA to specialized vectors
DNA ligase
limitation of cloning with restriction enzymes
modifications can only be made at restriction enzyme sites.
Through this method, foreign DNA can be
inserted into vectors (or the chromosome) by designing the insert
DNA to possess short regions (30–50 bases) of sequence homology
to the target DNA molecule and activating recombinase enzymes.
recombineering
(recombination-mediated genetic engineering)
a standard
cloning plasmid that contains an ampicillin resistance gene for selection and a blue–white color-screening system to select for recombinants. It also contains a short segment of artificial DNA containing
cut sites for many different restriction enzymes. This segment, called
a multiple cloning site (MCS), is inserted into the lacZ gene encoding
the lactose-degrading enzyme b-galactosidase
plasmid pUC19
colorless, can be
cleaved by b-galactosidase to generate a blue product in screening tests
X-gal (5-bromo-4-chloro-3-indolyl-b-d-galactopyranoside)
vectors can replicate and be stably maintained in two distinct organisms, such as
E. coli and yeast or E. coli and mammalian cells;
shuttle vectors
are linear vectors that
replicate in yeast like normal chromosomes but have sites where
very large fragments of DNA can be inserted.
yeast artificial
chromosomes (YACs)
Because
it is easy to grow and manipulate, the workhorse for cloning in
eukaryotic cells is the yeast
saccharomyces cerevisiae
However, if cloned gene expression is desired, the outer
membrane of this gram-negative bacterium can hinder protein secretion. This problem can be overcome using the
gram-positive bacterium as a cloning host
B. subtilis
are designed to allow the experimenter to control the expression of cloned genes.
expression vectors
are designed to allow the experimenter to control the expression of cloned genes.
expression vectors
introduce mutations at random in the DNA
of the intact organism
conventional mutagens
uses synthetic DNA plus DNA cloning techniques to
introduce mutations into genes at precisely determined sites.
site-directed mutagenesis
the gene encoding GFP was originally cloned
from the jellyfish
Aequorea victoria
a deficiency of somatotropin in the body results in
hereditary dwarfism
While recombinant DNA can be transformed into plant cells by
electroporation or transfection, the plasmid from the gram-negative bacterium Agrobacterium tumefaciens, a plant pathogen, can
be used to transfer DNA directly into the cells of certain plants.
Ti plasmid
Genetic engineering can modify a pathogen by deleting genes from its genome that encode
virulence factors while retaining those whose products elicit an immune response. This yields a recombinant and infective vaccine that is considered
attenuated because it is less virulent
than the original strain
one can add genes from a pathogenic virus to the genome
of a relatively harmless virus, called a carrier virus. Such vaccines are
called ??? and induce immunity to the pathogenic
virus.
vector vaccines
a vaccine
that immunizes against two different diseases at the same time.
polyvalent vaccine
vaccines that contain only a specific protein or
two from a pathogen, are also produced by recombinant means.
subunit vaccines
A set of genes that have all descended from a single ancestral gene
present in a shared ancestor are
homologs
Genes that are
highly similar in sequence often have the same function, and homologous genes that share the same function are orthologs.
orthologs
Genes that are homologous but have different
functions are
paralogs
Horizontal gene transfer is facilitated by this; it is the sum
total of all mobile genetic elements in a genome.
mobilome
genome segment; consisting of genes shared by all individual strains of a species
core genome
genome segment; consisting of the
core genome plus genes that are not shared by all strains of a species
pan genome
contain clusters of genes for specialized functions
chromosomal islands (also
called genomic islands)
Chromosomal islands that encode virulence factors, molecules that
facilitate disease and are found in pathogenic bacteria are called
pathogenicity islands
SSU rRNA genes remains a cornerstone of molecular phylogeny in microbiology because they are
highly conserved
present in all cellular organisms
easily sequenced and analyzed
Chemotrophic Metabolism; does not require an external electron acceptor and ATP is generated primarily by substrate-level
phosphorylation, with electron balance obtained by reducing metabolic intermediates that are then excreted as fermentation products
fermentation
Chemotrophic Metabolism;, requires an external electron acceptor, and ATP is generated by oxidative phosphorylation
resulting from electron transport reactions that generate a proton
motive force (pmf); the enzyme complex ATP synthase harnesses this
force to make ATP
respiration
The most important assimilative process in the biosphere
CO2 fixation performed by autotrophic organisms
most widespread and globally important pathway for CO2 fixation.
Calvin cycle
The key
enzyme of the Calvin cycle is the enzyme
RuBisCO
proteinaceous microcompartments and are
the site of RuBisCO activity.
carboxysomes
a pathway of CO2 fixation used by green sulfur bacteria such as Chlorobium, many anaerobic and microaerophilic
chemolithotrophic Bacteria
The reverse citric acid cycle (also called the reductive tricarboxylic acid cycle or rTCA cycle)
rTCA unique ezymes
a-ketoglutarate synthase and pyruvate synthase, which catalyze the
reductive fixation of CO2 using electrons supplied by Fdred.
TCA enzymes substituted in rTCA
citrate synthase with the enzyme
citrate lyase (an ATP-dependent enzyme that cleaves citrate into acetyl-CoA and oxaloacetate)
succinate dehydrogenase from the citric acid cycle by the FADH-linked fumarate reductase (an enzyme that forms succinate from fumarate) in the reverse cycle.
the most efficient of all CO2 fixation pathways
reductive acetyl-CoA
pathway
describes phototrophic organisms that consume H2O and produce O2 as a waste product; sometimes H2S to H2
oxygenic photosynthesis
describes photosynthetic organisms that do not produce O2
anoxygenic photosynthesis
contain magnesium instead of iron at the
center of the ring; contain specific substituents
on the tetrapyrrole ring and a hydrophobic alcohol that helps
anchor it into photosynthetic membranes.
chlorophylls
Anoxygenic phototrophs produce this chlorophyll equivalent
bacteriochlorophyll
In eukaryotic phototrophs,
photosynthesis takes place in intracellular organelles called
chloroplasts
chloroplasts,
which contain sheetlike photosynthetic membrane systems called
thylakoids
The ultimate structure for capturing energy from low light intensities is the
chlorosome
The most widespread accessory pigments in phototrophs; hydrophobic pigments that are
firmly embedded in the photosynthetic membrane
carotenoids
main light-harvesting systems of
these phototrophs
phycobiliproteins
results in noncyclic photophosphorylation because electrons do not cycle back to reduce the oxidized P680, but
instead are used in the reduction of NADP+
oxygenic photosynthesis
The reduced inorganic nitrogen compounds ammonia (NH3) and
nitrite (NO2
-) are oxidized aerobically by the chemolithotrophic
nitrifying bacteria in the process of
nitrification
NH3 can
alsobe oxidized under anoxic conditions. This process is called
anammox (for anaerobic ammonia oxidation) and is catalyzed by
an unusual group of obligately anaerobic Bacteria.
C1 assimilation pathway; acetyl-CoA is synthesized from
one molecule of CH2O and one molecule of CO2;
serine pathway
c1 assimilation pathway; more
energy efficient than the serine pathway because all of the carbon
for cell material is derived from CH2O
ribulose monophosphate pathway
yields a
single fermentation product, lactic acid.
homofermentative
yields products in addition to lactate, mainly
ethanol plus CO2.
heterfermentative
variant of glycolytic pathway; glucose 6-phosphate is oxidized
to 6-phosphogluconic acid and NADPH; the 6-phosphogluconic acid is dehydrated and split into pyruvate and glyceraldehyde
3-phosphate (G-3-P)
Entner–Doudoroff pathway
three different acids—acetic, lactic, and succinic—are formed from the fermentation of glucose or other sugars that can be converted into
glucose. Ethanol, CO2, and H2 are also typically formed as fermentation products;utilize glycolysis
mixed- acid fermentation
A number of clostridia ferment sugars, producing ??? and ??? as major fermentation products.
butyric acid, H2
