Chapter Sixteen: Bacterial Genes Flashcards
an adult human carries ___ bacteria, which is about the same as the number of human cells
30-50 trillion
most bacteria are in the ___, but they are also found in the ___, ___, and ___
intestines
skin, mouth, and respiratory tracts
___ are common for people with intestinal bacteria issues
fecal transplants
bacteria are ___ to ___ in length
200nm to 500micrometers
bacteria lack a ___ and ___
nucleus and membrane bound organelles
bacteria store their DNA in a single ___ folded into a ___
chromosome
nucleoid body
most bacteria have a ___, and some antibiotics inhibit ___ because human cells don’t have this characteristic
cell wall
cell wall synthesis
bacteria have adapted to a ___ of habitats
range
four possible habitats for bacteria
- on land
- in aquatic environments
- parasites
- symbionts inside another life form
bacterial ___ must be adapted to its environment
metabolism
some bacteria obtain energy from ___, others from ___
ammonia
sunlight
three natural processes that bacteria play a role in
- decomposition of materials for nutrient cycling
- important in nitrogen cycling
- some eat oil
bacteria that eat oil
bioremediation bacteria
a ___ fraction of bacteria is pathogenic
small
pathogenic bacteria invade ___ and produce ___
tissues
toxins
proteins that interfere with cell function or destroy cells
toxins
toxin that results in paralysis by interfering with communication between nerves and muscles
tetanus toxin
pretty much any bacteria that gets ___ will kill you
into your blood (septic)
the typical bacterial genome is composed of ___
one circular chromosome
there are ___ of DNA in most common studied bacteria
4-5Mb
the DNA molecule condenses by ___ and ___
supercoiling and looping
each bacterium replicates its chromosome and then divides by ___ into two daughter cells
binary fission
bacterial genomes are ___ with genes
tightly packed
___ of E. coli DNA encodes proteins; ___ of human DNA encodes proteins
90%
5%
E. coli have no ___ in their genome
introns
E. coli K12 genome has ___ genes
4288
genomes of ___ of E. coli strains have been sequences
100s
genes that are found in all strains of a species
core genome
there are about ___ core genes for E. coli
1000
functions of core genes
characteristics of life: nutrient assimilation, metabolism, waste removal, responding to environment, transcription and translation, replication, etc.
core genome plus all genes that are found in some strains of a species but not others
pangenome
the E. coli pangenome consists of about ___ genes
15,000
do bacterial genes contain transposons
yes
small bacterial transposons that do not contain selectable markers
insertion sequences (IS)
like the ends of DNA transposons in eukaryotic cells, the ends of IS elements are ___
inverted repeats of each other
each insertion sequence includes a gene that encodes ___
transposase
insertion sequences can disrupt ___
gene function
IS can rearrange bacterial genomes by causing ___ or ___
deletions or inversions
a bacterial transposon carrying transposase and drug resistance genes flanked by ISs
Tn elements
___ carry additional DNA
plasmids
plasmids are small circles of ___
double stranded DNA
plasmids are used as ___
cloning vectors
plasmids may contain genes that ___ or ___
benefit host bacterium or contribute to bacterial pathogenicity
plasmids that provide resistance to antibiotics
resistance plasmids
antibiotic resistance is often due to the presence of ___ on a plasmid
composite IS/Tn transposons
resistance plasmids can be transferred from ___ to ___ in nature easily
one bacteria to another
resistance plasmids are ___ for humans taking antibiotics
not good
the collective analysis of genomic DNA from an entire community of microbes
metagenomics
the initiative to identify all species of microorganisms that are symbionts with humans, and to correlate differences in microorganism populations with phenotypic differences and disease states
human microbiome project
there have been ___ species of bacteria identified in the human microbiome project
10,000
individuals vary in ___ of bacteria they carry
species
proteins that work under unusual conditions
extremophiles
a type of extremophile DNA polymerase
Taq DNA polymerase
extremophile bacteria that grow well in high pH have enzymes that are used in ___
laundry detergents
bacteria must be grown and studied in ___
cultures
bacteria are grown as ___ in liquid media
cell suspension
bacteria are grown as ___ on solid nutrient agar plates
colonies
the most studied and best understood bacterial species
E. coli
E. coli normally inhabits ___
intestines of warm-blooded animals
E. coli can grow in the complete absence of ___ or in ___
oxygen
air
lab strains of E. coli are not ___, but other strains can cause ___
pathogenic
intestinal diseases
E. coli are ___, meaning they can grow in minimal media
phototrophic
E. coli cells divide every ___
20 minutes
most bacteria carry ___ copy of each gene, making them ___
one
monoploid
because bacteria are monoploid, all mutations express ___
their phenotype
five categories of bacterial mutants
- affect colony morphology
- affect resistance to bactericides
- create auxotrophs
- affect catabolism
- affect essential genes
unable to reproduce in minimal media
auxotroph
mutations that create auxotrophs produce defective ___ that are required to synthesize complex compounds needed to survive
enzymes
a process that establishes conditions in which only the desired mutant will grow
genetic selection
a process in which colonies are examined for a particular phenotype
genetic screen
genes of bacteria specified by three lowercase italicized letters refer to the ___ of the gene
function
leuA, leuB, leuC, and leuD are genes that encode enzymes needed to synthesize ___
leucine
wild-type alleles are designated with ___ and mutant alleles are designated with ___
the passing or transferring of genes from parent to offspring, occurs in sexually reproducing organisms
vertical gene transfer
the introduction and incorporation of DNA from an unrelated individual or from a different species
horizontal gene transfer
three mechanisms for gene transfer in bacteria
- transformation
- conjugation
- transduction
bacterium that provides the DNA that is being transferred
donor
bacterium that receives the DNA, which can result in an altered phenotype
recipient
competent cells can take up DNA fragments from surrounding environment
transformation
when bacteria take up DNA fragments spontaneously from their environment
natural transformation
DNA transfer that can be accomplished in the lab by making the cells competent
artificial transformation
genes close together have a ___ of co-transformation than genes further apart
higher
donor DNA is transferred directly to the recipient through a connecting tube
conjugation
bacteria conjugation require ___
cell-to-cell contact
the ___ contains genes for synthesizing connections between donor and recipient cells
F plasmid
donors for conjugation are F___, meaning they carry a ___
+
F plasmid
recipients for conjugation are F___, meaning they do not carry a ___
-
F plasmid
process of conjugation
- F pilus binds to F- cell wall
- pilus retracts and cells are drawn together
- gene transfer occurs
after conjugation, both cells are ___ and can conjugate with other ___ cells
F+
F-
F plasmid has three ___, which are identical to those found at various positions on the bacterial chromosome
IS elements
formed when an F plasmid integrates into the bacterial chromosome through recombination between IS elements
high frequency recombinant (Hfr) cells
an F plasmid that can integrate into the bacterial genome
episome
Hfr strains differ in the ___ and ___ of the integrated episomes
location and orientation
Hfr strains retain all ___ and can be a ___ for conjugation with an F- strain
F plasmid functions
donor
transfer of DNA starts in the F plasmid at the ___
origin of transfer
___ located next to F plasmid sequences are transferred to the recipient
chromosomal sequences
transferred chromosomal DNA recombines into ___ in recipient
homologous DNA
process of gene transfer between Hfr donors and F- recipients
- F plus of Hfr cell establishes connection with F-cell
- single strand of integrated F plasmid is cut
- Hfr chromosome replicates itself as transfer happens
- F plasmid followed by chromosomal DNA passes into recipient cell
- donor DNA is replicated in host cell
- cells separate
- crossover between homologous regions on donor and recipient DNA
- recipient cell remains F- but carries some genes from Hfr chromosome
genes can be ___ by gene transfer during conjugation
mapped (located)
the ___ experiment was used to map genes by gene transfer in conjugation
interrupted-mating experiment
genes that immediately follow the origin of transfer in Hfr chromosome are ___
transferred first
order of transfer reflects the ___
gene order on the chromosome
a conjugative plasmid that carries many genes required for the transfer of DNA
F’ plasmid
F’ plasmid is formed by excision of ___ and ___
F plasmid and some adjacent bacterial chromosomal DNA
F’ plasmids replicate ___ in bacterial cells
independently
F’ plasmids can be transferred to F- cells by ___
conjugation
F’ plasmids can be used for ___ studies
complementation
cells carrying the F’ plasmid are called ___; cells without the F’ plasmid are called ___
F+
F-
conjugation of F- with F’ can make partial diploids called ___
merodiploids
merodiploids are partial diploids that contain ___
two copies of some genes
when assessing a mutation impacting tryptophan biosynthesis: if the merodiploid shown can grow without tryptophan, the two trp mutations are ___
in different genes
a method of transfer in which donor DNA is packed into a bacteriophage and transferred into the recipient when the phage infects it
transduction
phages are ___ in nature and most bacteria are susceptible to ___ phages
widely distributed
one or more
phages that always enter the lytic cycle after infecting a cell
virulent phages
phages that can enter either the lytic or lysogenic cycle after infecting a cell
temperate phages
the bacterial cycle of phage-infected cells resulting in cell lysis and release of progeny phage
lytic cycle
5 steps of the lytic cycle
- phage injects its DNA into bacterial cell
- phage proteins are expressed and take over protein synthesis and DNA replication machinery of infected cell
- phage DNA replication occurs
- phage particles are assembled with phage DNA and phage protein
- infected cell bursts and releases 100-200 new viral particles able to infect other cells
the population of phage particles released from host bacteria at the end of the lytic cycle
lysate
type of transduction that can result in the transfer of any bacterial gene between related strains of bacteria
generalized transduction
generalized transduction is the incorporation of ___ of bacterial DNA from donor into bacteriophage particles
random fragments
transfer of different bacterial genes together in one phage by transduction
cotransduction
frequencies of cotransduction depends directly on ___
the distance between the two genes
cotransduction frequencies are ___ for genes that are close together and ___ for genes that are further apart
higher
lower
for temperate phages, the choice between lytic or lysogenic phage depends on ___
many factors, including environmental conditions
bacteria that harbor in an integrated temperate phage
lysogen
temperate phage that has integrated into host chromosome
prophage
temperate phage commonly used in research
bacteriophage lambda
prophages do not produce the ___ needed for ___
viral proteins
more viral particles
lysogens can be induced to enter the ___
lytic cycle
how does a lysogen enter the lytic cycle
prophage is excised from chromosome, undergoes replication, and then new virus particles form
in some excisions of prophages, a small amount of ___ is excised with the prophage and packaged with viral DNA
bacterial genes adjacent to the prophage
bacteriophage carrying mainly phage DNA but also one or a few of the bacterial genes that lie near the site of prophage insertion
specialized transduction phages
bacteriophage-mediated transfer of a few bacterial genes located next to the prophage in the bacterial chromosome
specialized transduction
integration of ___ initiates the lysogenic cycle
phage lambda DNA
recombination between ___ on phage lambda and the bacterial chromosome allows integration of the prophage
att sites
___ produces a specialized transducing phage
abnormal excision
bacterial DNA adjacent to the integration site can be ___ with viral DNA and then ___ to recipient cell
packaged
transferred
___ is an important mechanism for rapid adaptation to environmental changes
gene transfer
genomic analysis has revealed ___ of gene transfer mechanisms in many bacterial species
widespread occurrence
large DNA segments transferred from one bacterial species to another
genomic islands
genomic islands originated from ___
horizontal gene transfer
many genomic islands contain genes that encode ___ and ___
integration-like enzymes and genes that promote fitness of the recipient
genes that promote fitness of the recipient are things like ___, ___
antibiotic resistant, metabolic enzymes
segments of DNA in disease-causing bacteria that encode several genes involved in pathogenesis
pathogenicity islands
Pathogenicity islands appear to have been transferred into the bacteria by horizontal gene transfer from a ___
different species
pathogenicity islands came from the lateral transfer of a package of genes from a ___ to a ___
pathogenic species
nonpathogenic species
can identify a mutant bacterial gene by ___ transformation
plasmid library
to identify the mutant in an arginine auxotroph, transform mutant bacteria with ___, identify clones that grow ___
plasmid genomic library
without arginine
gene ___ is used to make mutations in specific genes
targeting
penicillin interferes with ___
synthesis of the bacterial cell wall
penicillin binds to ___, inhibit its ___, and prevents ___
transpeptidase
enzymatic activity
cross-linking
N. gonorrhoeae acquired a plasmid from H. influenzae that had the ___
penicillin resistance gene (penr)
penr encodes ___
penicillinase
penA encodes ___, a mutation in this decreases ___
transpeptidase
affinity for penicillin
penB encodes ___, a mutation in this decreases ___
porin
entry of penicillin into cell
a porin is a ___ that regulates ___
protein in the outer cell wall
entry into the periplasm
mtr encodes ___, a mutation in this increases ___
repressor of an efflux pump
pumping of penicillin out of the cell
three things that combat the problem of drug resistance
- reduce antibiotic use
- develop novel classes of antibiotics
- make existing antibiotics more effective
MDRO stands for ___
multidrug resistant organism
